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The increasing concentration of nitrogen compounds in the groundwater is of a growing concern in terms of human health and groundwater quality. Although an excess of nitrogen compounds in the groundwater of the Kathmandu Valley has been reported, the seasonal variations of the fate of the nitrogen compounds and their relationships to the subsurface sediments are unknown. In this study, spatially distributed shallow dug well samples were collected during both the dry and wet seasons of 2016, and the nitrogen compound, chloride (Cl^−), and iron (Fe²⁺) concentrations were analyzed. Two shallow dug wells and one deep tube well were monitored monthly for 2 years. Although NH₄-N concentrations were similar in the clay-dominated areas during both seasons (1 and 0.9 mg-N/L), they were lower in the gravel-dominated areas during wet season (1.8 > 0.6 mg-N/L). The NO₃-N concentration differed depending upon the soil type which increased during the wet season (clay 4.9 < 13.6 mg-N/L and gravel 2.5 < 6.8 mg-N/L). The Fe²⁺ concentration, however, was low during the wet season (clay 2.7 > 0.4 mg/L and gravel 2.8 > 0.3 mg/L). Long-term analysis showed higher fluctuation of nitrogen compounds in the gravel-bearing areas than in the clay-bearing areas.