Re-eutrophication of Lake Erie: Correlations between tributary nutrient loads and phytoplankton biomass

Both abiotic and biotic explanations have been proposed to explain recent recurrent nuisance/harmful algal blooms in the western basin and central basin of Lake Erie. We used two long-term (> 10 years) datasets to test (1) whether Lake Erie total phytoplankton biomass and cyanobacterial biomass changed over time and (2) whether phytoplankton abundance was influenced by soluble reactive phosphorus or nitrate loading from agriculturally-dominated tributaries (Maumee and Sandusky rivers). We found that whereas total phytoplankton biomass decreased in Lake Erie's western basin from 1970 to 1987, it increased starting in the mid-1990s. Total phytoplankton and cyanobacterial seasonal (May–October) arithmetic mean wet-weight biomasses each significantly increased with increased water-year total soluble reactive phosphorus load from the Maumee River and the sum of soluble reactive phosphorus load from the Maumee and Sandusky rivers, but not for the Sandusky River alone during 1996–2006. During this same time period, neither total phytoplankton nor cyanobacterial biomass was correlated with nitrate load. Consequently, recently increased tributary soluble reactive phosphorus loads from the Maumee River likely contributed greatly to increased western basin and (central basin) cyanobacterial biomass and more frequent occurrence of harmful algal blooms. Managers thus must incorporate the form of and source location from which nutrients are delivered to lakes into their management plans, rather than solely considering total (both in terms of form and amount) nutrient load to the whole lake. Further, future studies need to address the relative contributions of not only external loads, but also sources of internal loading.     

The impact of phytoplankton community composition on optical properties and satellite observations of the 2017 western Lake Erie algal bloom

Since the early 2000s Lake Erie has seen a dramatic increase in phytoplankton biomass, manifested in particular by the rise in the severity of cyanobacteria blooms and the prevalence of potentially toxic taxa such as Microcystis. Satellite remote sensing has provided a unique capacity for the synoptic detection of these blooms, enabling spatial and temporal trends in their extent and severity to be documented. Algorithms for satellite detection of Lake Erie algal blooms often rely on a single consistent relationship between algal or cyanobacterial biomass and spectral indices such as the Maximum Chlorophyll Index (MCI) or Cyanobacteria Index (CI). Blooms, however, are known to vary significantly in community composition over space and time. A suite of phytoplankton and optical property measurements during the western Lake Erie algal bloom of 2017 showed highly diverse bloom composition with variable absorption and backscatter properties. Elevated backscattering coefficients were observed in the Maumee Bay, likely due to phytoplankton cell morphology and buoyancy regulating gas vacuoles, compared with typically Planktothrix dominated blooms in Sandusky Bay. MCI and CI calibrated to historical chlorophyll observations and applied to Sentinel 3's OLCI sensor accurately captured the 2017 bloom in Maumee Bay but underestimated the Sandusky Bay bloom by nearly 80%. The phycoerythrin-rich picocyanobacteria Aphanothece and Synechococcus were found in abundance throughout the western and central basins, resulting in substantial biomass underestimations using blue to green ratio-based algorithms. Potential misrepresentation of bloom severity resulting from phytoplankton optical properties should be considered in assessments of bloom conditions on Lake Erie.     

Structure and Ordination of Epiphytic Invertebrate Communities of Four Coastal Wetlands in Green Bay,Lake Michigan

Epiphytic macroinvertebrate communities of four coastal wetlands of Green Bay, Lake Michigan were compared by taxonomic composition, feeding group composition, and environmental influences using Bray-Curtis ordination. Ordination scores from the most sheltered oligotrophic site, Portage Marsh, were distinct from the eutrophic, exposed sites located in middle and lower Green Bay— Seagull Bar, Little Tail Point, and Dead Horse Bay. Epiphyton chlorophyll a, phytoplankton chlorophyll a, and specific conductance strongly correlated to the ordination axes, indicating the trophic gradient within Green Bay was a primary environmental influence. The feeding group compositions at the sites were consistent with the type and abundance of food available. Portage Marsh is a scraper-shredder system, with macroinvertebrates feeding mainly on epiphyton and coarse particulate detritus. Dead Horse Bay and Little Tail Point are collector systems, sustained by phytoplankton and fine particulate organic matter. Seagull Bar is intermediate in trophic position along the ordination axes, but more closely resemble the latter two sites. The type and abundance of food resources available to these invertebrate communities are influenced by wave exposure, light attenuation, nutrient levels, and algae levels of the littoral and pelagial waters. Macroinvertebrate communities were sensitive to shifts in food resources, which generated shifts in trophic structure.     

First evidence of grass carp recruitment in the Great Lakes Basin

We use aging techniques, ploidy analysis, and otolith microchemistry to assess whether four grass carp Ctenopharyngodon idella captured from the Sandusky River, Ohio were the result of natural reproduction within the Lake Erie Basin. All four fish were of age 1 +. Multiple lines of evidence indicate that these fish were not aquaculture-reared and that they were most likely the result of successful reproduction in the Sandusky River. First, at least two of the fish were diploid; diploid grass carp cannot legally be released in the Great Lakes Basin. Second, strontium:calcium (Sr:Ca) ratios were elevated in all four grass carp from the Sandusky River, with elevated Sr:Ca ratios throughout the otolith transect, compared to grass carp from Missouri and Arkansas ponds. This reflects the high Sr:Ca ratio of the Sandusky River, and indicates that these fish lived in a high-strontium environment throughout their entire lives. Third, Sandusky River fish were higher in Sr:Ca ratio variability than fish from ponds, reflecting the high but spatially and temporally variable strontium concentrations of southwestern Lake Erie tributaries, and not the stable environment of pond aquaculture. Fourth, Sr:Ca ratios in the grass carp from the Sandusky River were lower in their 2011 growth increment (a high water year) than the 2012 growth increment (a low water year), reflecting the observed inverse relationship between discharge and strontium concentration in these rivers. We conclude that these four grass carp captured from the Sandusky River are most likely the result of natural reproduction within the Lake Erie Basin.     

Cylindrospermopsis in Lake Erie: Testing its Association with Other Cyanobacterial Genera and Major Limnological Parameters

We report the first documented observation of the potentially toxic cyanobacterium Cylindrospermopsis in Lake Erie and Sandusky Bay in 2005 (0.043–1.326 mg L^-1 wet weight, 16–1,942 trichomes mL^-1) and quantify the physical and chemical parameters and the cyanobacterial community composition contemporaneous to its occurrence. We hypothesize that the high temperature, low light intensity, and high nutrient content of Sandusky Bay, a shallow, drowned river mouth along the southwestern shore of Lake Erie, provides an ideal habitat for Cylindrospermopsis. This is consistent with published laboratory and field studies that show these physical and chemical conditions facilitate Cylindrospermopsis growth. Using multivariate statistics, we found that Cylindrospermopsis biomass correlated with high temperatures and shallow depths, conditions often found in Sandusky Bay. Light climate and nutrient concentrations were not associated with Cylindrospermopsis biomass, most likely because the light climate did not systematically change during the season and because nutrients exceeded demand. We propose that Cylindrospermopsis will increase in importance in Lake Erie, as previous research on climate change in the Great Lakes region predicts future higher water temperatures and lower water levels.     

Philopatry and vagrancy of white bass (Morone chrysops) spawning in the Sandusky River: Evidence of metapopulation structure in western Lake Erie using otolith chemistry

Although natal homing and philopatry are well studied in anadromous salmon, few studies have investigated philopatric behavior in large, freshwater systems. In western Lake Erie, white bass (Morone chrysops) undergo seasonal spawning migrations from the open-water regions of Lake Erie to nearshore reef complexes and tributaries. The three primary spawning locations in Lake Erie are within 80 km of each other and are not separated by physical barriers. We used naturally occurring differences in otolith strontium concentrations among major spawning locations to address philopatry and vagrancy to the Sandusky River spawning location. Most individuals spawning in the Sandusky River were natal to this river (73%). No statistically significant differences in the extent of homing by sex or age of spawning were found, although a potential pattern of decreased homing with increased age of fish was observed. Given the proportion of vagrant individuals we found spawning in the Sandusky River (27%), it is unlikely that Lake Erie white bass spawning populations are genetically distinct. Furthermore, the white bass population in Lake Erie appears to be structured as a metapopulation, with non-philopatric individuals serving as a link between spawning populations.     

Phosphorus loading to Lake Erie from the Maumee,Sandusky and Cuyahoga rivers: The importance of bioavailability

Lake Erie has undergone re-eutrophication beginning in the 1990s, even though total phosphorus (TP) loads to the lake continued to slowly decline. Using our 1982 and 2007–10 studies of the bioavailability of dissolved and particulate phosphorus export from major Ohio tributaries, together with our long-term TP and dissolved reactive phosphorus (DRP) loading data, we estimated long-term annual export of dissolved and particulate bioavailable phosphorus. DRP was found to adequately represent dissolved bioavailable export while 26–30% of the particulate phosphorus (PP) was extractable by 0.1 N NaOH, a frequently used indicator of PP bioavailability. During the period of re-eutrophication (1991–2012), DRP export from nonpoint sources in the Maumee and Sandusky rivers increased dramatically while NaOH-PP export had a slight decline for the Maumee and a small increase in the Sandusky. For the Cuyahoga River, both DRP and NaOH-PP increased, but these changes were small in relation to those of the Maumee and Sandusky. During this period, whole lake loading of both non-point and point sources of phosphorus declined. This study indicates that increased nonpoint loading of DRP is an important contributing factor to re-eutrophication. Although nonpoint control programs in the Maumee and Sandusky have been effective in reducing erosion and PP export, these programs have been accompanied by increased DRP export. Future target loads for Lake Erie should focus on reducing bioavailable phosphorus, especially DRP from nonpoint sources. Agricultural P load reduction programs should address both DRP and PP, and take into account the lower bioavailability of PP.     

Glyphosate influence on phytoplankton community structure in Lake Erie

In this study we investigated the effect of the phosphonate herbicide glyphosate (N-(phosphonomethyl)glycine) on the phytoplankton community structure in Lake Erie using lake water incubations, laboratory growth experiments and phylogenetic analysis of phosphonate metabolism genes. In microcosms, addition of glyphosate to Sandusky Bay water resulted in a significant increase in phytoplankton abundance, specifically causing an increase in the abundance of Planktothrix spp. In microcosms using Maumee Bay water, glyphosate did not stimulate phytoplankton growth but caused a decrease in Microcystis spp. abundance. The difference in the ability of Planktothrix spp. and Microcystis spp. to grow in the presence of glyphosate was confirmed in laboratory growth experiments. Further, an examination of the molecular pathways involved in phosphonate metabolism demonstrated that heterotrophic bacteria may be critical in allowing this proliferation. The results indicate that glyphosate has both positive and negative influences on phytoplankton community structure, serving as a nutrient source to microbes able to tolerate the herbicidal effects of the compound while killing those less tolerant. Moreover, this work highlights that in natural environments microorganisms function as communities, and the metabolic abilities of individual species are often less important than the collective ability of the community.     

Tributary use and large-scale movements of grass carp in Lake Erie

Infrequent captures of invasive, non-native grass carp (Ctenopharyngodon idella) have occurred in Lake Erie over the last 30+ years, with recent evidence suggesting wild reproduction in the lake’s western basin (WB) is occurring. Information on grass carp movements in the Laurentian Great Lakes is lacking, but an improved understanding of large-scale movements and potential areas of aggregation will help inform control strategies and risk assessment if grass carp spread to other parts of Lake Erie and other Great Lakes. Twenty-three grass carp captured in Lake Erie’s WB were implanted with acoustic transmitters and released. Movements were monitored with acoustic receivers deployed throughout Lake Erie and elsewhere in the Great Lakes. Grass carp dispersed up to 236 km, with approximately 25% of fish dispersing greater than 100 km from their release location. Mean daily movements ranged from <0.01 to 2.49 km/day, with the highest daily averages occurring in the spring and summer. The Sandusky, Detroit, and Maumee Rivers, and Plum Creek were the most heavily used WB tributaries. Seventeen percent of grass carp moved into Lake Erie’s central or eastern basins, although all fish eventually returned to the WB. One fish emigrated from Lake Erie through the Huron-Erie Corridor and into Lake Huron. Based on our results, past assessments may have underestimated the potential for grass carp to spread in the Great Lakes. We recommend focusing grass carp control efforts on Sandusky River and Plum Creek given their high use by tagged fish, and secondarily on Maumee and Detroit Rivers.     

Otolith microchemistry shows natal philopatry of walleye in western Lake Erie

Natal philopatry is important to the structure of fish populations because it can lead to local adaptations among component stocks of a mixed population, reducing the risk of recruitment failure. By contrast, straying between component stocks may bolster declining populations or allow for colonization of new habitat. To examine rates of natal philopatry and straying among western Lake Erie walleye (Sander vitreus) stocks, we used the concentration of strontium [Sr] in otolith cores to determine the natal origin of adults captured at three major spawning sites: the Sandusky (n = 62) and Maumee (n = 55) rivers and the Ohio reef complex (n = 50) during the 2012–2013 spawning seasons. Mean otolith core [Sr] was consistently and significantly higher for individuals captured in the Sandusky River than for those captured in the Maumee River or Ohio reef complex. Although logistic regression indicates that no individuals with a Maumee River or Ohio reef complex origin were captured in the Sandusky River, quadratic discriminant analysis suggests low rates of straying of fish between the Maumee and Sandusky rivers. Our results suggest little straying and high rates of natal philopatry in the Sandusky River walleye stock. Similar rates of natal philopatry may also exist across western Lake Erie walleye stocks, demonstrating a need for stock-specific management.     

Maternal and stock effects on egg-size variation among walleye Sander vitreus stocks from the Great Lakes region

Fish egg sizes vary intra-specifically among stocks and individuals, and such variation may reflect a combination of maternal and environmental influences. As egg size variation has important implications for individual and population recruitment success, it is useful to quantify egg-size variation and identify potential factors underlying such variation. We evaluated 1) within-stock maternal influences on egg size and 2) the relative elucidatory power of maternal effects versus stock in explaining inter-individual mean egg size based on eggs collected during 2007–2008 from five walleye Sander vitreus stocks in the North American Laurentian Great Lakes region. We used both linear regression models and classification and regression trees (CART) to describe egg-size variation. Egg size tended to increase with female length and for some stocks was greatest for intermediate maternal ages. However, maternal influences on egg size were relatively low and variable between years. In contrast, stock had a stronger effect; walleye egg-size variation was greater among stocks than within stocks. After controlling for the influence of maternal age and length, we found that egg size was relatively small for fish spawning in Maumee and Sandusky Rivers (western Lake Erie), intermediate in Oneida Lake and Tittabawassee River (Saginaw Bay, Lake Huron), and relatively large in Van Buren Bay (eastern Lake Erie) and Little Bay de Noc (northern Green Bay, Lake Michigan). Such inter-stock differences in maternal influence adjusted egg size appeared to be negatively associated with a system's productivity; suggesting a potential adaptive response of egg size to early life habitat conditions.     

The relative importance of anammox and denitrification to total N2 production in Lake Erie

Production of dinitrogen gas via microbially mediated anaerobic ammonium oxidation (anammox) and denitrification plays an important role in removal of fixed N from aquatic ecosystems. Here, we investigated anammox and denitrification potentials via the ¹⁵N isotope pairing technique in the helium flushed bottom water (~0.2 m above the sediment) of Sandusky Bay, Sandusky Subbasin, and Central Basin in Lake Erie in three consecutive summers (2010?2012). Potential rates of anammox (0–922 nM/day) and denitrification (1 to 355 nM/day) varied greatly among sampling sites during the 3 years we studied. The relative importance of anammox to total N₂ production potentially ranged from 0 to 100% and varied temporally and spatially. Our study represents one of the first efforts to measure potential activities of both anammox and denitrification in the water column of Lake Erie and our results indicate the Central Basin of Lake Erie is a hot spot for N removal through anammox and denitrification activities. Further, our data indicate that the water column, specifically hypolimnion, and the surface sediment of the Lake Erie Central Basin are comparatively important for microbially mediated N removal.     

Unionid mussels from nearshore zones of Lake Erie

Concern exists that the introduction of dreissenid mussels following long-term effects of pollution may have completely eliminated native mussel species from Lake Erie. Natural seiche events were used to facilitate surveys for live unionids on five occasions in the western basin of Lake Erie and Sandusky Bay between 2007 and 2009, and beach and estuary surveys were conducted at numerous additional sites between 2004 and 2009. Sixteen unionid species were found living in or near Lake Erie, including six sites in the nearshore zone of the lake. Each community consisted of live individuals from two to eight species, and evidence included live and/or fresh dead material from several state listed species at multiple sites. Where estimated, the mean overall density was low at 0.09 unionids/m², although similar to other known unionid refuges in the lower Great Lakes. While the ephemeral nature of seiche events makes them a limited survey tool, their application combined with increasing numbers of fresh shells washing ashore over the past few years indicates that unionids are extant in the western basin of Lake Erie, and may further suggest that conditions may be improving for native mussel species.     

A matrix population model to aid agency response to grass carp (Ctenopharyngodon idella) in the Great Lakes Basin - Lake Erie

Managers and researchers have identified a reproducing population of grass carp (Ctenopharyngodon idella) in the western basin of Lake Erie, generating concern over the potential threat to ecosystem function in the Great Lakes Basin. Capture histories indicate that grass carp may be present at low levels in other areas of Lake Erie, necessitating a large scale, multi-jurisdictional response. As a result, a group of experts and decision makers began a structured decision making exercise to collaboratively address the threat and identify potential response actions. To aid this process, we developed a spatially-explicit periodic matrix population model to project grass carp abundance, and probabilistically evaluate specific management actions. We evaluated four potential management response actions ranging from no action, diffuse removal efforts, and concentrated removal efforts with and without a barrier on the Sandusky River to reduce spawning success. Based on our current knowledge, concentrated removal including a barrier on the Sandusky River provides the most likely path to achieving and maintaining a management target of no more than 10 fish/ha. Our understanding of grass carp ecology in Lake Erie is growing. This model and parameter development methods were designed to flexibly accommodate new information as our understanding of grass carp ecology evolves, or management objectives change. Ultimately, this modeling framework and use of Bayesian methods could facilitate management response efforts for other invasive species occurring over large scales and multiple jurisdictions.     

Proliferation of phytoplankton along a 500 km transect of the St. Lawrence River from its outflow at Lake Ontario

Observation of phytoplankton and water chemistry along the main channel of the St. Lawrence River was made at a high spatial resolution (every 12 km) in order to infer the factors that influence development of this phytoplankton community. The phytoplankton community in the main channel was collected over a 10-d period (mid July 2018) from the headwaters to near the beginning of the St. Lawrence River estuary. Total phosphorus concentration in river water increased with distance downstream (154–2,750 nM) and phytoplankton biomass (1.4–10.5 µg chl-a/L) was strongly correlated (r = 0.84, 46 d.f.) to the concentration of total phosphorus. Diatoms, chrysophytes and dinoflagellates dominated the phytoplankton community at the outlet of Lake Ontario and total chlorophyll-a concentrations increased three-fold with 500 km transit downstream from Lake Ontario; phycocyanin-rich Cyanobacteria showed the greatest proportional increase (227%). Total P concentrations observed in 1997 along this transect were identical to those observed in 2018; however, chl-a concentrations were much lower in 1997, a finding attributed to a greater filter feeding benthic organism impact on the standing crop of phytoplankton. Observations support the hypothesis that the phytoplankton community composition in this large river is strongly influenced by the headwater characteristics (Lake Ontario) and gradually influenced by entrainment of nutrient-rich tributary waters.     

Post-tournament dispersal of smallmouth bass in western Lake Erie

Catch-and-release tournaments for smallmouth bass Micropterus dolomieu transport fish from many capture locations to a centralized release site. In the Great Lakes, these fish may be transported long distances (i.e., >100 km) and subsequently become concentrated at a release site, possibly negatively affecting subpopulations at popular fishing sites if fish remain concentrated in the area. To assess timing of post-tournament dispersal, 23 smallmouth bass were implanted with acoustic transmitters and released into Sandusky Bay (Lake Erie) after a large tournament (50 boats) in September 2018. Tagged fish were tracked via a grid of acoustic receivers. All surviving fish (n = 19) left the immediate vicinity of the release site (<500 m) after an average (±SE) of 13.2 (±2.4) d, with many (58%) returning to the main lake (19.7 d ± 3.4). Eight (42%) of the surviving fish left the release site but remained in the bay after 50 d. Based on the results from this study, long-term (>1 month) concentration of smallmouth bass at release sites is unlikely to be a problem for Lake Erie bass tournaments, but temporary (up to 1 month) accumulations of fish are possible. A fraction of tournament-released smallmouth bass resided in Sandusky Bay for extended periods (>2 months), which could be considered functionally harvested from main lake subpopulations. Currently, the frequency of bass tournaments on Lake Erie is uncertain, and better documentation of tournament frequency and scale is necessary to assess potential negative impacts on bass populations.     

Estimating the Extent of Reduction Needed to Statistically Demonstrate Reduced Non-Point Phosphorus Loading to Lake Erie

The need to reduce non-point phosphorus contributions to Lake Erie has led to extensive efforts to implement conservation tillage in the Lake Erie basin. Because annual loads are highly variable, statistical approaches will be required to document the success of conservation tillage and other best management practices in reducing loads. Important management issues are how large a reduction will be required, and how long it will take to achieve the needed reduction. In response to these issues, a method is presented for estimating the amount of change needed to establish a statistically significant reduction, based on the standard t-test. Analysis of data from the Sandusky River, a north-central Ohio tributary of Lake Erie, indicates that the necessary change is about 35% of the current loads. When the loads are adjusted for variations in discharge, the necessary change can be reduced to about 20%. Based on projections of the Army Corps of Engineers of adoption rates of conservation tillage, and the associated effects on phosphorus loads, a 35% change would take 25 years or more, but a 20% change would occur by the end of 8 years. The documentation of these changes will require high quality monitoring data, collected before and during the implementation period with the same sampling strategy.     

Evidence for a Trophic Cascade Effect on North-shore Western Lake Erie Phytoplankton Prior to the Zebra Mussel Invasion

Increasing summer total phosphorus (TP) concentrations measured in samples from a municipal water intake off the north shore of western Lake Erie during 1976 to 1983 were inconsistent with TP loads to the western basin of Lake Erie and with phytoplankton densities in the intake samples, both of which declined over the same time interval. The long-term (1976 to 1988) summer TP data were inversely correlated (r = −0.858) with summer average maximum daily wind velocities, suggesting that low wind velocities contributed to anoxia at the sediment-water interface and high sediment TP release rates in summer. While TP loading reductions in the late 1960s and early 1970s likely contributed to phytoplankton declines, continued phytoplankton declines during the late 1970s to early 1980s could not have been caused by continued reductions in TP loadings while TP concentrations increased. The phytoplankton declines of the 1980s are more likely attributable to changes in the trophic cascade associated with dramatic declines in some species of zooplanktivorous fish during the 1970s and 1980s as a result of a restored walleye population. Long term phytoplankton densities were fit (R² = 0.902) to a multiple regression model with western Lake Erie TP loads and an index of zooplanktivore density as independent variables; the zooplanktivore component of this model was the most significant contributor to the prediction of phytoplankton density. The implications of these findings for maintenance of good lake water quality include the need to maintain strong piscivore populations as well as reduced phosphorus loads.     

Updated phosphorus loads from Lake Huron and the Detroit River: Implications

The binational Great Lakes Water Quality Agreement (GLWQA) revised Lake Erie’s phosphorus (P) loading targets, including a 40% western and central basin total P (TP) load reduction from 2008 levels. Because the Detroit and Maumee River loads are roughly equal and contribute almost 90% of the TP load to the western basin and 54% to the whole lake, they have drawn significant policy attention. The Maumee is the primary driver of western basin harmful algal blooms, and the Detroit and Maumee rivers are key drivers of central basin hypoxia and overall western and central basin eutrophication. So, accurate estimates of those loads are particularly important. While daily measurements constrain Maumee load estimates, complex flows near the Detroit River mouth, along with varying Lake Erie water levels and corresponding back flows, make measurements there a questionable representation of loading conditions. Because of this, the Detroit River load is generally estimated by adding loads from Lake Huron to those from the watersheds of the St. Clair and Detroit rivers and Lake St. Clair. However, recent research showed the load from Lake Huron has been significantly underestimated. Herein, I compare different load estimates from Lake Huron and the Detroit River, justify revised higher loads from Lake Huron with a historical reconstruction, and discuss the implications for Lake Erie models and loading targets.     

Diversity and ecology of phytoplankton in Lake Edward (East Africa): Present status and long-term changes

Lake Edward is one of the African Rift Valley lakes draining into the Nile River basin. We conducted three sampling series in Lake Edward in October-November 2016, March-April 2017 and January 2018, in distinct seasonal conditions and in several sites varying by depth and proximity to river outlets, including the Kazinga Channel, which connects the hypertrophic Lake George to Lake Edward. The phytoplankton was examined using microscopy and marker pigment analysis by high performance liquid chromatography (HPLC) and subsequent CHEMTAX processing for estimating abundance of phytoplankton groups. Chlorophyll a concentration in the pelagic and littoral open lake sites barely exceeded 10 µg L⁻¹ whereas, in contrast, in the semi-enclosed Bay of Katwe influenced by the Kazinga Channel chlorophyll a was up to 100 µg L⁻¹. Despite substantial seasonal variations of limnological conditions such as photic and mixed layer depths, cyanoprokaryotes/cyanobacteria represented on average 60% of the phytoplankton biomass, followed by diatoms, which contributed ~25% of chlorophyll a, and by green algae, chrysophytes and cryptophytes. 248 taxa were identified with clear prevalence of cyanobacteria (104 taxa), from the morphological groups of coccal and filamentous species (non-heterocytous and heterocytous). The high proportion of heterocytous cyanobacteria, along with a relatively high particulate organic carbon to nitrogen (C:N) ratio, suggest N limitation as well as light limitation, most pronounced in the pelagic sites. During the rainy season, the most abundant diatoms in the plankton were needle-like Nitzschia. Comparison with previous studies found differences in water transparency, total phosphorus, and phytoplankton composition.