Groundwater nitrate (NO3−) pollution sources and in situ attenuation were investigated in Kisumu city and Kano plains. Samples from 62 groundwater wells consisting of shallow wells (hand dug, depth <10 m) and boreholes (machine drilled, depth >15 m) were obtained during wet (May–July 2017) and dry (February 2018) seasons and analyzed for physicochemical and isotopic (δ15N-NO3−, δ18O-NO3−, and δ11B) parameters. Groundwater NO3− concentrations ranged from <0.04 to 90.6 mg L−1. Boreholes in Ahero town showed significantly higher NO3− (20.0–70.0 mg L−1) than boreholes in the Kano plains (<10.0 mg L−1). Shallow wells in Kisumu gave significantly higher NO3− (11.4–90.6 mg L−1) than those in the Kano plains (<10.0 mg L−1). About 63% of the boreholes and 75% of the shallow wells exceeded the drinking water WHO threshold for NO3− and NO2− (nitrite) during the study period. Mean δ15N-NO3− values of 14.8‰ ± 7.0‰ and 20.7‰ ± 11.1‰, and δ18O-NO3− values of 10.2‰ ± 5.2‰ and 13.2‰ ± 6.0‰ in wet and dry seasons, respectively, indicated manure and/or sewage as main sources of groundwater NO3−. However, a concurrent enrichment of δ15N and δ18O was observed, especially in the dry season, with a corresponding NO3− decrease, indicating in situ denitrification. In addition, partial nitrification of mostly sewage derived NH4+ appeared to be responsible for increased NO2− concentrations observed in the dry season. Specifically, targeted δ11B data indicated that sewage was the main source of groundwater NO3− pollution in shallow wells within Kisumu informal settlements, boreholes in Ahero, and public institutions in populated neighborhoods of Kano; while manure was the main source of NO3− in boreholes and shallow wells in the Kano and planned estates around Kisumu. Waste-water sanitation systems in the region should be urgently improved to avoid further deterioration of groundwater sources.

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