Lakes are vital freshwater ecosystems that sustain biodiversity, support livelihoods, and drive socio-economic growth globally. However, they face escalating threats from anthropogenic activities, including urbanization, agricultural runoff, and pollution, which are exacerbated by climate change. Phewa Lake in Nepal was selected for this study due to its increasing rates of nutrient enrichment, sedimentation, and pollution. This study evaluated seasonal and spatial water quality variations within the lake by analyzing water samples from 30 sites during the pre-monsoon and post-monsoon seasons. Twenty physicochemical parameters, including the potential of hydrogen (pH), dissolved oxygen (DO), electrical conductivity (EC), and major ions, e.g., calcium (Ca²⁺), magnesium (Mg²⁺), sodium (Na⁺), potassium (K⁺), bicarbonate (HCO₃⁻), chloride (Cl⁻), sulfate (SO₄²⁻), nitrate (NO₃⁻), phosphate (PO₄³⁻), and ammonium (NH₄⁺), were measured. The average pH ranged from 8.06 (pre-monsoon) to 8.24 (post-monsoon), reflecting dilution from monsoon rains and increased carbonate runoff. Furthermore, the DO levels in Phewa Lake averaged 7.46 mg/L (pre-monsoon) and 8.62 mg/L (post-monsoon), with higher values observed post-monsoon due to rainfall-driven oxygenation. Nutrient concentrations were shown to be elevated, with the nitrate concentration reaching 2.31 mg/L during the pre-monsoon period, and the phosphate concentration peaking at 0.15 mg/L in the post-monsoon period, particularly near agricultural runoff zones. The dominant cations in the lake’s hydrochemistry were Ca²⁺ and Mg²⁺, while HCO₃⁻ was the primary anion, reflecting the influence of carbonate weathering. Cluster analysis identified the lake outlet as a high-pollution zone, with the total dissolved solids (TDS) reaching 108–135 mg/L. Additionally, Principal component analysis revealed agricultural runoff and sewage effluents as the main pollution sources. Seasonal dynamics highlighted monsoon-induced dilution and pre-monsoon pollution peaks. These findings underscore the need for targeted pollution control and eutrophication management. By aligning with the sustainable development goals (SDGs) relevant to clean water and climate action, this research provides a replicable framework for sustainable lake management that is applicable to freshwater ecosystems worldwide.