The eastern Niger Delta region in Nigeria is a hotspot for reactive nitrogen pollution due to extensive animal husbandry, pit latrine usage, and agricultural practices. Despite the high level of human activity, the sources and processes affecting nitrogen in groundwater remain understudied. Groundwater nitrate (NO3−) concentrations are highly variable, with some areas recording values well above the safe drinking water threshold of 50 mg/L. This is particularly true near municipal sewage systems. Elevated nitrite (NO2−) and ammonium (NH4+) concentrations were also detected in the study area. Sewage analysis revealed NO3− concentrations ranging from 1 to 145 mg/L, NO2− from 0.2 to 2 mg/L, and notably high NH4+ concentrations. A comparison of major ions indicated that 71%, 90%, 87%, and 92% of groundwater samples surpassed reference site levels for calcium (Ca2+), sodium (Na+), potassium (K+), and chloride (Cl−), respectively, pointing to sewage as a likely source of contamination. The NO3−/Cl− ratios at several sites suggested that most groundwater NO3− originates from human waste. Stable isotope analysis of NO3− showed a general enrichment in 15N and, in some cases, a depletion in 18O, indicating that the NO3− originates from sewage-derived NH4+ nitrification. Although denitrification, a process that reduces NO3−, is present, the high dissolved oxygen (DO) and NO3− levels in the groundwater suggest that denitrification is insufficient to fully mitigate NO3− pollution. Consequently, there is a risk of NO3− leaching from shallow aquifers into the Niger Delta’s surface waters and ultimately into the coastal ocean.