Four high altitude lakes i.e Sella Lake, Pangang Tang Tso Lake, Shungatser Lake and Tskyo Tso Lake located at an altitude of 3962 metres in the Eastern lesser Himalaya were monitored for seasonal variation in hydrogeochemical processes and effective CO₂ pressure in order to understand the imprints of climate change. A comparative scenario of water quality among high altitude Himalayan lakes has been also presented. In the post-monsoon season, all major cations increased whereas major anions except NO₃⁻ increased in the lake system. The results revealed that major cations in the lakes in post-monsoon increased whereas major anions except NO₃⁻increased in post-monsoon. During pre-monsoon, Ca-HCO₃ type and Ca-Mg-SO₄ type were the major faces of lake water which changed to Na-SO₄ and Ca-Na-HCO₃ type in post-monsoon. It was found that wet precipitation of aerosols is the most important source of major ions followed by chemical weathering. The pCO₂ has increased in the post-monsoon probably due to higher atmospheric CO₂ during winter than that of rainy season. Factor analysis revealed that weathering, anthropogenic are the main governing process in the pre-monsoon whereas evaporative enrichment and geochemical inputs are the main process in the post-monsoon season. ANOVA analysis showed significant difference for pH, EC, SO₄²⁻, NO₃⁻, Na⁺, K⁺ indicating input from evaporative enrichment, weathering and long range transport of pollution to lake system.