A study was conducted to assess the potential of nitrate-nitrogen (NO
3-N) and fluoride (F) contamination in drinking groundwater as a function of lithology, soil characteristics and agricultural activities in an intensively cultivated district in India. Two hundred and fifty two groundwater samples were collected at different depths from various types of wells and analyzed for pH, electrical conductivity (EC), NO
3-N load and F content. Database on lithology, soil properties, predominant cropping systems, fertilizer and pesticide uses were also recorded for the district. The NO
3-N load in groundwater samples were low ranging from 0.12 to 6.58 μg mL
− 1 with only 8.7% of them contained greater than 3.0 μg mL
− 1 well below the 10 μg mL
− 1, the threshold limit fixed by WHO for drinking purpose. Samples from the habitational areas showed higher NO
3-N content over the agricultural fields. The content decreased with increasing depth of wells (
r = − 0.25,
P ≤ 0.01) and increased with increasing rate of nitrogenous fertilizer application (
r = 0.90,
P ≤ 0.01) and was higher in areas where shallow- rather than deep-rooted crops (
r = − 0.28,
P = ≤ 0.01, with average root depth) are grown. The NO
3-N load also decreased with increasing bulk density (
r = − 0.73,
P ≤ 0.01) and clay content (
r = − 0.51,
P ≤ 0.01) but increased with increasing hydraulic conductivity (
r = 0.68,
P ≤ 0.01), organic C (
r = 0.78,
P ≤ 0.01) and potential plant available N (
r = 0.82,
P ≤ 0.01) of soils. Fluoride content in groundwater was also low (0.02 to 1.15 μg mL
− 1) with only 4.0% of them exceeding 1.0 μg mL
− 1 posing a potential threat of fluorosis. On average, its content varied little spatially and along depth of sampling aquifers indicating little occurrence of F containing rocks/minerals in the geology of the district. The content showed a significant positive correlation (
r = 0.234,
P = ≤ 0.01) with the amount of phosphatic fertilizer (single super phosphate) used for agriculture. Results thus indicated that the groundwater of the study area is presently safe for drinking purpose but some anthropogenic activities associated with intensive cultivation had a positive influence on its loading with NO
3-N and F.
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