Plankton is an important component of lake food webs. Their carbon and nitrogen stable isotope values can reflect the fluctuation of biogeochemical cycling and food sources and can be applied to track the changes of aquatic ecosystem structure. In this paper, four lakes with distinct typology from Yunnan Province were selected to uncover the seasonal changes in carbon and nitrogen stable isotopic compositions of plankton. The carbon stable isotope values of phytoplankton in large deep lakes (Lake Fuxian and Lake Yangzong) are enriched in summer and autumn (mean ±SD: -20.34‰±1.98‰), but relatively depleted in winter and spring (-28.00‰±2.51‰), which may reflect a higher growth rate of plankton and greater assimilation of bicarbonate (HCO₃^-) during the growing season. In small shallow lakes (Lake Changqiao and Lake Datun), carbon stable isotopic values of phytoplankton are mostly enriched in summer (-21.24‰±0.88‰) among the four sampling seasons. This may be related to the increased input of terrigenous organic matter during the rainy season, and a decreased lower water level due to overuse of agricultural irrigation in summer. In contrast to the carbon stable isotope values, the nitrogen stable isotope composition of plankton displayed a similar trend of seasonal variations across lakes where a significantly more positive value was found in spring than in other seasons. Further analyses revealed that that seasonal variation in the nitrogen stable isotope of plankton is related to the seasonal difference of nitrogen sources and their distinct isotopic compositions. Specifically, non-point source pollution, mainly related to agricultural fertilizers with depleted nitrogen stable isotopic value, is often dominant in the rainy season, while point source pollution predominantly derived from sewage input with enriched nitrogen stable isotopic composition is commonly observed in the dry season. In terms of stable isotope fractionation between zooplankton and phytoplankton (i.e. trophic enrichment), small shallow lakes were characterized by smaller carbon (1.61‰±0.90‰) and nitrogen (2.71‰±1.22‰) stable isotopic enrichment than those in large deep lakes (2.60‰±0.98‰ and 4.19‰±1.25‰, respectively) in this study. Zooplankton often displays a higher degree of dependence on autochthonous organic carbon (such as phytoplankton) with increasing nutrient status, reflecting a stronger coupling of organic carbon transfer between trophic levels. Similarly, a smaller degree of nitrogen stable isotope enrichment is evidenced in more eutrophic lakes in this study.