The current study investigates groundwater contamination in Darrang district, situated in the flood-prone Brahmaputra Valley. This research evaluates the concentrations and geospatial distributions of iron, fluoride, and arsenic in groundwater samples (n = 347) and assesses their potential ecotoxicological risks to human health. Multivariate statistical techniques were used to investigate the sources and the mobilization mechanism of the contaminants in the aquifer system. The Piper and Gibbs plots reveal that silicate weathering, ion exchange, and mineral dissolution are the dominant processes influencing groundwater chemistry. Notably, higher pH levels (max = 8.5, mean = 7.4) are associated with alkaline desorption of arsenic from minerals. Cluster analysis also indicates the occurrence of pH induced carbonate weathering process implying weathering and active dissolution as a governing mechanism for arsenic release. The health risk assessments indicate significant non-carcinogenic and carcinogenic risks from prolonged exposure to arsenic, particularly for children. Spatial distribution maps identify areas most at risk of contamination and related health hazards. This is the first comprehensive analysis of groundwater contaminants in Darrang, providing valuable insights into the region’s water quality issues and supporting future groundwater management efforts in Brahmaputra floodplain region.