The study is undertaken to assess the groundwater quality in the alluvial region of the Yamuna basin, mainly comprising unconsolidated sand, silt and clays. A total of 14 and 13 water samples were collected in pre- and post-monsoon seasons, respectively, from handpumps, tubewells, ponds and irrigated fields to assess the water quality for human consumption and identify possible sources of contaminants in water. According to the Gibbs diagram, the ionic composition of water is mainly dominated by the rock weathering processes. The major hydrochemical facies is Ca–Mg–HCO3 type. The scatter plots between Ca+Mg:SO4+HCO3 and Na:Cl indicate the occurrence of silicate weathering which is supported by HCO3/HCO3+SO4 ratio <1. Manganese (Mn) concentration in 57% and 54% water samples in pre- and post-monsoon season exceeds the permissible limit i.e. 0.3 mg/L. Further, high iron (Fe) concentration (up to 33.5 mg/L) is also detected mainly in the shallow groundwater. The presence of higher Mn and Fe concentrations in the water samples is generally associated with the regions having low or negative redox values. Additionally, their positive correlation with sulphate and chloride ions indicates their occurrence as sulfates and chlorides. The results signify the role of regional geology in the presence of these ions in water along with the secondary influence of agricultural and anthropogenic activities (human and animal waste) on the quality of shallow groundwater. The Water Quality Index varies greatly, from excellent to unsuitable category in both seasons mainly due to the presence of high Fe and Mn content in shallow handpumps, village pond and a few tubewells located in the agricultural fields. Leaching of fertilizers and fungicides in the agricultural fields may further contribute in deteriorating shallow groundwater quality.