THE INFLUENCE OF VARIABLE HABITAT SUITABILITY CRITERIA ON PHABSIM HABITAT INDEX RESULTS

The Physical Habitat Simulation System (PHABSIM) still probably remains as the most widespread habitat method used to establish inflow standards or to link habitat temporal variations with fish population dynamics. However, statistical uncertainties around the PHABSIM main output, the weighted usable area (WUA) over discharge curves, are usually ignored. Here, we assess the uncertainty in WUA curves and derived habitat duration curves induced by the variability around the PHABSIM biological model, the habitat suitability criteria, using brown trout Salmo trutta as the model species. Bootstrap analyses showed that the uncertainty around the WUA curves was rather high when bootstrap sample (BS) size was low and differed among age classes, being generally lower for young‐of‐the‐year (YOY). Width of 95% confidence intervals for maximum WUA magnitude increased with decreasing BS size, ranging from 19.3% for YOY trout at the largest BS size (40 transects, 270 habitat use observations) to 146% for juveniles at the smallest BS size (nine transects, 60 habitat use observations). The uncertainty arose primarily from the construction of the channel index variable. Nevertheless, results showed that the uncertainty in WUA values could be reduced down to acceptable levels by using general functional channel index categories. Likewise, the shape of WUA curves was also highly variable when BS was small. These patterns resulted in habitat duration curves being highly uncertain, much more in their amplitude than in their shape. Uncertainty about the flows corresponding to different habitat exceedance values increased with decreasing probability of exceedance. Width of peak flow confidence intervals ranged from 3.3% for YOY trout at the largest BS size to 226% for adults at the smallest BS size. Yet such levels of uncertainty do not necessarily entail critical errors in the decision‐making process because large variability in flow peak does not necessarily lead to large variability in WUA magnitude.     

Using habitat guilds to develop habitat suitability criteria for a warmwater stream fish assemblage

The diversity of fish species found in warmwater stream systems provides a perplexing challenge when selecting species for assessment of instream flow needs from physical habitat analyses. In this paper we examined the feasibility of developing habitat suitability criteria (HSC) for the entire fish community of a warmwater stream using habitat guilds. Each species was placed a priori into a guild structure and habitat data were collected for depth, velocity, Froude number, distance to cover, embeddedness and dominant and subdominant substrate. Correct guild classification was tested with linear discriminant analysis for each species. Correct classification based on habitat‐use data was highest for riffle and pool‐cover guilds, whereas the fast‐generalist and pool‐run classes, the broader niche guilds, were more frequently misclassified. Variables most important for discriminating guilds were Froude number, velocity and depth in that order. Nonparametric tolerance limits were used to develop guild suitability criteria for continuous variables and the Strauss linear index was used for categorical variables. We recommend the use of a wide array of variables to establish more accurate habitat analysis. Additionally, guild HSC can be developed with similar effort to that needed to develop HSC for a small number of individual species. Results indicate that a habitat guild structure can be successfully transferred to another river basin and that habitats for a diverse fish assemblage can be adequately described by a small number of habitat guilds. This approach represents an alternative for incorporating entire fish assemblages into habitat analyses of warmwater stream systems. Copyright © 2010 John Wiley & Sons, Ltd.     

Instream flow determination using a multiple input fuzzy‐based rule system: a case study

The attempts made to manage water to meet human requirements should also consider the needs of freshwater species and ecosystems. There are many tools available to assess instream flow needs, one of which is the use of habitat preference models. In this study, a fuzzy approach was used for modelling habitat preferences for two life stages of Atlantic salmon (Salmo salar). Experienced fish biologists and technicians contributed to the development of fuzzy sets and fuzzy preference rules for spawning and parr habitat. Fuzzy sets were defined for water depth, velocity and substrate composition. Fuzzy preference rules for the two life stages were then defined as sets of IF–THEN rules relating the physical attributes to habitat suitability. The fuzzy suitability indices are then used to obtain weighted usable area (WUA) at different discharges and to estimate the ecologic flow required to preserve habitat. Different methods are applied to combine the membership function and rules defined by the experts. A sensitivity analysis of rules of the combined system indicated that a limited number of rules are determinant and results are highly dependent on the consequences of these rules. A modification in the consequence of these rules can significantly alter WUA estimations. It is therefore recommended to combine the knowledge of many experts in the elicitation process and to quantify the uncertainty associated with the combination of expert knowledge. Copyright © 2007 John Wiley & Sons, Ltd.     

Habitat suitability curves for brown trout (Salmo trutta fario L.) in the River Adda,Northern Italy: comparing univariate and multivariate approaches

Habitat suitability of brown trout (Salmo trutta fario) was studied in the upper portion of the Adda River, Northern Italy. Measurements were made for 528 individuals distributed in two life‐stage classes, adult and juvenile, based on body length. In order to provide basic biological information for the physical habitat simulation (PHABSIM) system of the instream flow incremental methodology (IFIM) in the Italian regulated rivers, habitat suitability curves (HSCs) have been developed with respect to several microhabitat riverine parameters. Initially, current velocity, water depth, substrate class size and cover were analysed with an univariate approach, then bivariate habitat suitability models were developed from depth and velocity data. The comparison of experimental univariate HSCs with those from the literature outlined some differences that can essentially be explained by characteristics of the investigated river, confirming the necessity of using site‐specific curves in relation to each experimental study area. To compare the univariate and bivariate approaches, the weighted usable area (WUA)–discharge relationships were calculated using both types of HSCs. Response curves obtained from the two approaches turned out to be quite different. In PHABSIM habitat modelling, HSCs univariate functions need to be aggregated to produce the WUA–discharge relationship. A multiplicative criterion is generally used for the combined suitability factor; by means of this aggregation criterion all variables have equal weight. According to bivariate models, depth is much more important than velocity in defining habitat suitability requirements. Copyright © 2001 John Wiley & Sons, Ltd.     

Two‐dimensional modelling of habitat suitability as a function of discharge on two Colorado rivers

The quantity of water that should be retained in streams and rivers for the benefit of fish during periods of water scarcity is a question of considerable interest to river managers and biologists. Although instream flow methodologies have existed since the 1970s, no single method has been widely accepted for use on large warm‐water rivers because of their high species richness and generalized fish habitat use patterns. In this paper, we present an approach similar to instream flow incremental methodology, but which uses two‐dimensional flow models and biomass estimates derived from multiple sites on two Colorado rivers for predicting the effect of discharge on adult standing stocks of two native fish species. Suitability criteria are developed for bluehead and flannelmouth sucker (Catostomus discobolus and C. latipinnis) by comparing adult biomass in individual meso‐habitat units with modelled depths and velocities. We find that roundtail chub (Gila robusta) biomass is not correlated with depth and velocity, but appears to be positively associated with indices of habitat heterogeneity. Species biomass and total usable habitat area are predicted as a function of discharge for each site and data show good correlation between predicted and measured biomass. Results suggest that the Colorado and Yampa Rivers have similar potential for native fish biomass, but low summer discharges limit native fish biomass on the Yampa River. Copyright © 2005 John Wiley & Sons, Ltd.     

Lost in space,the sequel: spatial sampling issues with 1‐D PHABSIM

The Physical Habitat Simulation System (PHABSIM) is a popular method for evaluating the habitat value of a stream in terms of a statistic, weighted usable area (WUA). Usually, PHABSIM is used with one‐dimensional (1‐D) hydraulic models, and curves of WUA over discharge are calculated at transects and combined to produce a composite curve. Curves of WUA over discharge are often presented as evidence in proceedings to determine instream flow requirements, so the reliability of these curves is important. Representing a reach of stream with transects introduces ordinary statistical questions: is the sample of transects unbiased, and is it large enough to produce usefully precise estimates? Unfortunately, these questions are seldom considered in PHABSIM studies, even though most PHABSIM studies characterize streams with fewer than 15 transects. Moreover, transect locations usually are selected deliberately, so estimates of WUA will usually be biased. This paper extends an earlier analysis of the uncertainty in composite WUA curves with a much larger set of transect curves, with more analysis of uncertainty in the shape of the WUA curves, and with a different method for simulating errors in estimates of WUA at the transects. The results show that even with larger than usual numbers of transect curves, the precision of composite WUA curves is likely to be poor, especially if there are errors in the transect WUA curves. I also offer suggestions regarding sampling, and for estimating the number of transects that might be needed to achieve a given level of precision in WUA estimates. Copyright © 2009 John Wiley & Sons, Ltd.     

A MODEL INCORPORATING DISTURBANCE AND RECOVERY PROCESSES IN BENTHIC INVERTEBRATE HABITAT—FLOW TIME SERIES

We describe and demonstrate a model (Benthic Invertebrate Time Series Habitat Simulation) for calculating the effect of changes to flow regimes on benthic invertebrate habitat and population dynamics. The following inputs are required: a hydrograph (discharge time series), habitat–discharge relationship, disturbance–discharge relationship, wetted width–discharge relationship and a recolonization time series. Habitat–discharge, disturbance–discharge and wetted width–discharge relationships are common outputs from instream hydraulic habitat models (e.g. Physical Habitat Simulation, River Hydraulic Habitat Simulation and River2D). Hydraulic habitat models calculate a combined habitat suitability index from physical habitat suitability curves for water depth, velocity and substrate composition and weight this by area to give a weighted usable area (WUA). Because conventional invertebrate habitat suitability curves are based on density estimates, the combined habitat suitability index can be treated as an index of density and WUA treated as an index of potential relative abundance (at the reach scale) in the absence of disturbance due to flow variation (flooding and drying) and biotic processes. Our approach begins with WUA and calculates realizable suitable habitat (i.e. relative abundance) by taking into account the resetting of benthic invertebrate densities by floods and drying and recovery (or accrual) rates and times. The approach is intended mainly to compare the relative amounts of productive invertebrate habitat sustained by natural and modified flow regimes, but it also has the potential for investigating the influence of flow variation on invertebrate population dynamics. We anticipate that the model will be particularly useful for assessing effects of changes in flow regimes caused by diversions, abstractions or water storage on annual benthic invertebrate productivity. Copyright © 2013 John Wiley & Sons, Ltd.     

Comparison of MesoHABSIM with two microhabitat models (PHABSIM and HARPHA)

This study demonstrates how using different habitat models can influence the results of instream habitat assessment and conclusions for river management. We used three models for a portion of the Quinebaug River (Connecticut and Massachusetts, USA): a simplistic microhabitat model with univariate habitat‐use criteria and substrate‐based channel index (the Physical Habitat Simulation Model (PHABSIM)); a microhabitat model using multivariate criteria including a wide range of cover attributes (HARPHA); and a mesohabitat model with multivariate habitat‐suitability criteria (MesoHABSIM). The flow‐habitat rating curves produced by each model were compared at two scales: site and study segment. To investigate the impact of model choice on answering questions such as which location or flow provides more habitat, we applied Spearman's correlation of ranks. The relationship between habitat‐suitability predictions and fish presence at the same location was investigated with dedicated fish observations. The study showed that: (1) of the tested models, only MesoHABSIM predictions correlated with fish observations; (2) the variation within microscale models (PHABSIM and HARPHA) was greater than between micro‐and mesoscale models (HARPHA and MesoHABSIM); and (3) simple univariate habitat‐use criteria provided the largest source of discrepancies among the models. We suggest that these differences may lead to erroneous conclusions, especially if flow‐habitat rating curve analysis is considered an endpoint of instream flow study. Copyright © 2007 John Wiley & Sons, Ltd.     

USE OF HYDRAULIC MODELLING TO ASSESS PASSAGE FLOW CONNECTIVITY FOR SALMON IN STREAMS

The maintenance of hydrologic connectivity in river networks has become an important principle for guiding management and conservation planning for threatened salmon populations, yet our understanding of how fish movement is impaired by spatial and temporal variation in connectivity remains limited. In this study, a two‐dimensional hydraulic modelling approach is presented to evaluate flow connectivity in relation to passage requirements of adult steelhead trout (Oncorhynchus mykiss) in coastal California streams. High‐resolution topographic data of stream reaches with distinct channel morphology were collected using terrestrial light detection and ranging surveys and linked with water surface measurements to calibrate hydraulic model simulations. Quantitative metrics of longitudinal flow connectivity were developed to assess fish passage suitability in relation to stream discharge. Measured flow data from the 2008–2009 winter season and simulated long‐term records indicated that suitable passage flows occur with relatively low frequency and duration at all sites, suggesting that instream flow protections for fish passage are warranted. Results from the hydraulic modelling simulations were then compared with two alternative methods for assessing passage flows. A regional formula used by the State of California to identify minimum instream flow needs provided conservative estimates of passage flow requirements, whereas an approach based on riffle crest water depths underestimated flow needs. The hydraulic modelling approach appears well suited for simulating flows for fish passage studies and may be particularly useful for testing alternative environmental flow assessment methods and evaluating habitat–flow relationships in stream reaches of importance, such as critical habitat for threatened fish species. Copyright © 2011 John Wiley & Sons, Ltd.     

Applying instream flow incremental method for the spawning habitat protection of Chinese sturgeon (Acipenser sinensis)

The Chinese sturgeon, Acipenser sinensis, is an anadromous species that spawns in the Yangtze River and Pearl River of China. Its population has declined dramatically since the construction of the Gezhouba Dam (GD) in 1981 and then with the impoundment of the Three Gorges Dam (TGD) upstream of the GD in 2003. This paper presents a quantitative method based on the instream flow incremental method to explore the relationship between the fish spawning habitat and the operations of the GD and TGD, aiming to find a solution for conservation of the species. A two‐dimensional hydrodynamic model was built with the River2D to simulate the hydraulic behaviour of the stream below the GD. Habitat suitability index was determined by the biological data of the fish collected in the field. The two parts were then integrated through a geographical information system developed via ArcGIS to outline the fish habitat area variation with flows. The decision support system is applied to set up a habitat time series for validating the assumption that more habitats have the potential to support more fish. The fish habitat results for alternative instream flow schemes are then compared with one another for defining the optimal flow requirements and evaluating effects of reservoir operation alternatives in order to improve the operation management for the GD and TGD projects. The results show that the optimal flow for spawning of the fish is about 7000–13000 m³/s and the optimal inlets combination is where the inflow comes from two power plants. Copyright © 2009 John Wiley & Sons, Ltd.     

Variability in flow–habitat relationships as a function of transect number for PHABSIM modelling

A bootstrap analysis was used to assess the variability in flow–habitat relationships for juvenile and adult rainbow trout (Oncorhynchus mykiss) in the Cache La Poudre River as a function of the number of Physical Habitat Simulation System (PHABSIM) transects. The bootstrap analysis was conducted by selecting without replacement different numbers of transects, ranging from six to 40, from a pool of 107 transects. The variability in flow–habitat relationships, as quantified by the 95% confidence interval for the flow with the peak habitat, decreased with increasing numbers of transects, and was greater for juveniles than for adults. The 95% confidence limits ranged from 9% for adult trout with 40 transects to 73% for juvenile trout with six transects. The results of this study can be used in negotiations for the number of transects selected during scoping of instream flow studies, as well as in assessing the relative confidence that should be placed in flow–habitat relationships for different species and life stages. Published in 2005 by John Wiley & Sons, Ltd.     

Comparison of methods for analysing salmon habitat rehabilitation designs for regulated rivers

River restoration practices aiming to sustain wild salmonid populations have received considerable attention in the Unites States and abroad, as cumulative anthropogenic impacts have caused fish population declines. An accurate representation of local depth and velocity in designs of spatially complex riffle‐pool units is paramount for evaluating such practices, because these two variables constitute key instream habitat requirements and they can be used to predict channel stability. In this study, three models for predicting channel hydraulics—1D analytical, 1D numerical and 2D numerical—were compared for two theoretical spawning habitat rehabilitation (SHR) designs at two discharges to constrain the utility of these models for use in river restoration design evaluation. Hydraulic predictions from each method were used in the same physical habitat quality and sediment transport regime equations to determine how deviations propagated through those highly nonlinear functions to influence site assessments. The results showed that riffle‐pool hydraulics, sediment transport regime and physical habitat quality were very poorly estimated using the 1D analytical method. The 1D and 2D numerical models did capture characteristic longitudinal profiles in cross‐sectionally averaged variables. The deviation of both 1D approaches from the spatially distributed 2D model was found to be greatest at the low discharge for an oblique riffle crest with converging cross‐stream flow vectors. As decision making for river rehabilitation is dependent on methods used to evaluate designs, this analysis provides managers with an awareness of the limitations used in developing designs and recommendations using the tested methods. Copyright © 2008 John Wiley & Sons, Ltd.     

Application of physical habitat simulation (PHABSIM) modelling to modified urban river channels

Prediction of changes to in‐stream ecology are highly desirable if decisions on river management, such as those relating to water abstractions, effluent discharges or modifications to the river channel, are to be justified to stakeholders. The physical habitat simulation (PHABSIM) system is a well‐established hydro‐ecological model that provides a suite of tools for the numerical modelling of hydraulic habitat suitability for fish and invertebrate species. In the UK, the most high‐profile PHABSIM studies have focused on rural, groundwater‐dominated rivers and have related to low flow issues. Conversely, there have been few studies of urban rivers. This paper focuses on the application of PHABSIM to urban rivers and demonstrates how sensitivity analyses can be used to assess uncertainty in PHABSIM applications. Results show that physical habitat predictions are sensitive to changes in habitat suitability indices, hydraulic model calibration and the temporal resolution of flow time‐series. Results show that there is greater suitable physical habitat over a wider range of flows in a less engineered river channel when compared to a more engineered channel. The work emphasizes the need for accurate information relating to the response of fish and other organisms to high velocities. Copyright © 2004 John Wiley & Sons, Ltd.     

A survey of methods for setting minimum instream flow standards in the Caribbean basin

To evaluate the current status of instream flow practices in streams that drain into the Caribbean Basin, a voluntary survey of practising water resource managers was conducted. Responses were received from 70% of the potential continental countries, 100% of the islands in the Greater Antilles, and 56% of all the Caribbean island nations. Respondents identified ‘effluent discharges’, ‘downstream water quality’ and ‘existing extraction permits’ to be the most common sources of instream flow conflicts. In 75% of the countries, some type of ‘formal procedures’ exist for reviewing permit applications for freshwater extraction. In 82% of the countries, effluent discharge permits state the amount of effluent that can be discharged into a water body while only 69% require that surface water extraction permits explicitly state the quantity of water that can be extracted. In setting instream flow requirements, record low flow is used over 83% of the time. Freshwater fish were identified as the most important aquatic organism but no country ‘always’ considers the ecology or habitat requirements of aquatic species in their instream flow determinations and nearly 70% of the respondents indicated that multivariate, ecological‐based methods are ‘never’ used in their country. Survey responses also indicate there is a notable lack of public involvement during the issuing of water permits. Moreover, over 80% of the countries do not provide public announcements or hearings during the permit process. In summary, this survey indicates that while there is a widespread recognition of the need for instream flows, there is a general lack of regionally based information and public involvement regarding stream flow determination. Copyright © 2003 John Wiley & Sons, Ltd.     

History and review of the habitat suitability criteria curve in applied aquatic ecology

Hydraulic microhabitat assessment is a category of environmental flow tools (e.g., Physical Habitat Simulation system and other methodologically similar software) that, at its core, uses habitat suitability criteria (HSC) to link values of point hydraulic variables (usually depth, velocity, and substrate/cover) to habitat values for target life stages. Although this assessment tool has been used worldwide for decades, the history of the HSC curve is relatively unknown because the foundational information is predominantly contained in obscure and often unpublished reports. We review the history of the HSC concept in applied aquatic ecology to clarify its scientific pedigree, ensure its proper use, and build a foundation for future research. We begin the review with the formative decades of the 1950's through the 1970's, when consumptive‐based western USA water law conflicted with conservation traditions and natural resource management objectives, although water allocation issues date back at least to the 19th century. By analysing the history of the HSC concept, we aim to establish the biological, hydrologic, and geomorphological conditions that must be met for the HSC concept to be successfully employed. In spite of its documented assumptions and limitations, the HSC concept will likely continue to be a useful tool to help address water resources allocation issues in defined hydrologic and geomorphic settings. We conclude that HSC‐based methodologies should be considered as one of several environmental flow approaches involved in sustainable water resources management.     

The basic flow method for incorporating flow variability in environmental flows

The Basic Flow is a methodology used to calculate environmental flow needs for river regulation. It has gained increased recognition in Spain for hydrological planning. It is based on the study of irregularities in hydrological series of daily mean flows using the simple moving average model as a tool to extract the relevant information. The Basic Flow Methodology (BFM), beyond providing a unique minimum flow value, constitutes a complex management proposal for regulated rivers which includes other management aspects affecting the biological functioning of a river (such as the necessity of flow variability, bankfull flows or varying flow rates) through the establishment of monthly instream flow requirements. This paper presents a practical application of the BFM in the Silvan stream, a natural mountain stream impacted by a hydroelectric regulation project. Results are discussed in terms of physical habitat created and compared to those obtained from the application of another method based on the Instream Flow Incremental Methodology, using a set of computer programs (RHYHABSIM) for physical habitat simulation. Copyright © 2010 John Wiley & Sons, Ltd.     

Predicted Native Fish Response,Potential Rewards and Risks from Flow Alteration in a New Mexico Arid Mountain Stream

Water and natural resource managers are concerned with evaluating how fish habitat and populations may respond to water diversions and small‐scale flow augmentations. We used two‐dimensional hydraulic models, habitat suitability curves and an individual‐based population viability model to assess whether flow augmentations of about 0.28–0.57 m³/s would create suitable habitat for federally listed native fish loach minnow Rhinichthys cobitis and spikedace Meda fulgida in a reach of the Gila River, New Mexico, and then examined how fish population viability may change under a variety of colonization and extinction scenarios. These simulations help to inform water management decisions in a reach of the Gila River where river diversions currently exist and new diversions and augmentations are being proposed. Our results suggest that the flow augmentations evaluated will result in small changes (on average across life stages, ?0.22% to 4.06%) in suitable habitat for loach minnow and spikedace depending on augmentation scenario and fish life stage. While these percent changes are small, they would result in a reduction in the dewatering of the river channel in a river reach where native fish abundance is thought to be low. Actual native fish responses to these habitat changes are unknown; however, these flow augmentations could potentially allow these native species to re‐colonize this river segment from upstream or downstream sources increasing species distribution and likely population viability. Maintaining viable populations of native fish in this river reach is dependent on complex factors including persistence of suitable habitat for multiple life stages, connectivity with other populations and minimizing risk of invasion from non‐native species. We recommend that these predictions from the habitat and population models be tested and verified in an adaptive management framework linking modelling, experimental management, monitoring and reassessment to inform water management decisions in the Gila River. Copyright © 2017 John Wiley & Sons, Ltd.     

A review of statistical methods for the evaluation of aquatic habitat suitability for instream flow assessment

Habitat models serve three main purposes: First, to predict species occurrences on the basis of abiotic and biotic variables, second to improve the understanding of species‐habitat relationships and third, to quantify habitat requirements. The use of statistical models to predict the likely occurrence or distribution of species based on relevant variables is becoming an increasingly important tool in conservation planning and wildlife management. This article aims to provide an overview of the current status of development and application of statistical methodologies for analysing the species‐environment association, with a clear emphasis on aquatic habitat. It describes the main types of univariate and multivariate techniques available for analysis of species‐environment association, and specifically focuses on the assessment of the strengths and weaknesses of the available statistical methods to estimate habitat suitability. A second objective of this article is to propose new approaches using existing statistical methods. A wide array of habitat statistical models has been developed to analyse habitat‐species relationship. Generally, physical habitat is dependent on more than one variable (e.g. depth, velocity, substrate, cover) and several suitability indices must be combined to define a composite index. Multivariate approaches are more appropriate for the analysis of aquatic habitat as they inherently consider the interrelation and correlation structure of the environmental variables. Ordinary multiple linear regression and logistic regression are popular methods often used for modelling of species and their relationships with environment. Ridge regression and Principal component regression are particularly useful when the independent variables are highly correlated. More recent regression modelling paradigms like generalized linear models (GLMs) present advantages in dealing with non‐normal environmental variables. Generalized additive models (GAMs) and artificial neural networks are better suited for analysis of non‐linear relationships between species distribution and environmental variables. The fuzzy logic approach presents advantages in dealing with uncertainties that often exist in habitat modelling. Appropriate methods for analysis of multi‐species data are also presented. Finally, the few existing comparative studies for predictive modelling are reviewed, and advantages and disadvantages of different methods are discussed. Copyright © 2006 John Wiley & Sons, Ltd.     

Spatial scales in instream flow modeling: Why and how to use ecologically appropriate resolutions

This paper discusses why and how to use ecologically appropriate spatial resolutions (e.g., cell size or range of cell sizes) when modeling instream flow effects on aquatic animals. Resolution is important because relations between habitat and animal habitat use vary with spatial resolution, and different habitat variables may best predict habitat use at different resolutions. Using appropriate resolutions consistently would bring clarity and coherence to how we quantify and model habitat characteristics and habitat use by fish, facilitate the use of standard and more credible measures of habitat preference, incorporate more fisheries knowledge to improve models for different kinds of fish, and avoid well-known (and perhaps unknown) biases. Doing so involves describing habitat, and habitat use by fish, with spatially explicit measures with clear resolutions; using the same resolution for physical habitat and fish habitat use; selecting that resolution for ecological reasons; and using habitat variables and fish observation methods appropriate for the resolution. The choice of resolution considers factors such as how much space fish use for specific activities and the size of important habitat patches. For drift-feeders, cell sizes and fish habitat use observations should use a resolution no smaller than feeding territories. Piscivores typically hunt over large areas so should be modeled with larger habitat units. Models of small and less-mobile organisms (e.g., benthic invertivores) may need fine resolutions to capture the small areas of unusual habitat they depend on. Because of such differences, instream flow studies (like any spatial ecology exercise) should clearly state what resolution(s) they use and why.