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This study identified the sources of fecal contamination in the groundwater of different land covers. A total of 300 groundwater samples were collected in the Kathmandu Valley, Nepal, in the dry (<i>n =</i> 152) and wet (<i>n =</i> 148) seasons of 2016. Fecal indicator bacteria were initially enumerated, and then fecal contamination sources were identified using human (BacHum), ruminant (BacR), and pig-associated (Pig2Bac) <i>Bacteroidales</i> quantitative polymerase chain reaction assays. Sixty-six percent (197/300) of the tested groundwater samples had <i>Escherichia coli</i> concentrations higher than the World Health Organization threshold for drinking (&lt;1 most probable number/100 mL). The fecal contamination of the groundwater was of human (22%, 55/250), ruminant (11%, 28/250), and pig (3%, 8/250) origin. Deep tube wells were less likely to be positive for <i>E. coli</i> and fecal markers compared to shallow dug wells. The human fecal marker was more likely to be detected in sources from built-up as compared to agricultural areas (Adjusted odds ratio (AOR) = 3.60, <i>p</i> = 0.002). Likewise, the ruminant fecal marker was more likely to be detected in sources from agricultural as compared to built-up areas (AOR = 2.90, <i>p</i> = 0.018). These findings suggest the preparation of mitigation strategies for controlling fecal pollution based on land cover and well types.