Human activities and climate change increasingly threaten wetlands worldwide, yet their hydrochemical properties and water quality are often inadequately studied. This research focused on the Ghodaghodi Lake Complex (GLC) and associated lakes in Nepal, a Ramsar-listed site known for its biodiversity and ecological significance. The study was conducted to assess seasonal water quality, investigate the factors influencing hydrochemistry, and assess the lakes’ suitability for irrigation. Forty-nine water samples were collected from the GLC in pre-monsoon and post-monsoon periods. Nineteen physicochemical parameters, such as dissolved oxygen (DO), total dissolved solids (TDS), and major ions (calcium ‘Ca2+’, magnesium ‘Mg2+’, and bicarbonate ‘HCO3−’), were analyzed using standard on-site and laboratory methods. Statistical methods, including analysis of variance (ANOVA), T-tests, and hydrochemical diagrams, e.g., Piper, were adopted to explore spatial and seasonal variations in water quality, revealing significant fluctuations in key hydrochemical indicators. Results showed marked seasonal differences, with pre-monsoon TDS levels averaging 143.1 mg/L compared to 78.9 mg/L post-monsoon, underscoring evaporation and dilution effects. The hydrochemical analysis identified Ca2+-HCO3− as the dominant water type, highlighting the influence of carbonate weathering on GLC’s water composition. Gibbs, mixing, and Piper diagram analysis supported these findings, confirming the predominance of HCO3−, with Ca2+ and Mg2+ as the main cations. Additionally, sodium adsorption ratio (SAR) values were consistently below 1, confirming excellent irrigation quality. These findings provided critical data for policymakers and stakeholders, supporting sustainable wetland management and aligning with the United Nations’ Sustainable Development Goals relevant to environmental conservation, i.e., clean water and life on land.