We evaluated the thermal and chemical stratifications of Paldang Lake using Schmidt’s stability index (SSI) and the chemical stratification index (IC-i) with weekly data from 2013 to 2022. The temporal trends of stratification were analyzed alongside correlations with meteorological, hydrological, and water quality variables. Thermal stratification intensified with rising air temperature and sunshine duration, while hydrological factors like discharge and retention time affected SSI during periods with less than five days of water retention. During summer, fewer occurrences of intense rainfall or early rainfall before August led to stronger stratification. In fall, nutrient influx from external sources during summer stimulated algal growth, increasing Chlorophyll-α (Chl-α) concentrations. Summer rainfall had a significant impact on the strength and duration of stratification in Paldang Lake. Annual rainfall patterns and subsequent changes in discharge were key factors affecting the physical environment of the lake, which in turn determined water quality and the extent of algal blooms. We provide insights into the seasonal stratification and water quality variations in temperate river-type reservoirs like Paldang Lake. SSI and IC-i from this research can be applied to understand stratification and mixing dynamics in other lakes.