© 2022, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.Freshwater scarcity, deterioration and associated water management remain to be one of the most challenging aspects of high-population density economies especially in subtropical/tropical regions. The present research deals with hydrogeochemical analysis of the eco-sensitive Baraila wetland and possible sources of anthropogenic pollution. The hydrochemical characterization was performed in GIS environment, considering meteorologically induced parameters and spatial variability. Temporal variations were assessed through different seasons, namely pre-monsoon, monsoon and post-monsoon with the help of multivariate statistics. The changes in water depth across the seasons showed significant hydrochemical variations in the vertical profile of the wetland apart from thermal demarcation. Seasonal variations in the hydrogeochemistry were induced by multiple physicochemical parameters, geochemical processes, geomorphology of the surrounding area and land use and land cover (LULC) changes. The pre-post flooding changes revealed that aquatic vegetation was increased by 15.36% whereas a major decrease in water bodies (− 73.2%) occurred. Dissolved oxygen (DO), pH, temperature and carbonates are fundamental towards establishing wetland’s water chemistry. The water type is primarily of Ca-HCO3 type, mostly derived from rock-water interactions and cation exchange processes. Irrigational quality of water was assessed through multiple indices (sodium adsorption ratio (SAR), %Na, residual sodium carbonate (RSC), magnesium hazard (MH) and total hardness (TH)) and plots. The heavy aquatic vegetation abundance and eutrophication because of agricultural run-off is currently the major issue with the Baraila wetland and may be playing a simultaneous role in regulating the water chemistry to a large extent apart from other geochemical processes. The hydrogeochemical interactions between sediment and overlying water have created distinct effects on biota and land use/land cover changes. Their role in the landscape is prominent in this respect and may be utilized for environmental management, eco-tourism and employment boost. Serious lack of hydrogeochemical studies in this important floodplain wetland and its rapid deterioration deems it necessary to focus on the comprehensive research and wetland management options for its conservation and sustainable usage in future.