The Caohai Wetland serves as an important ecosystem on the Yunnan–Guizhou Plateau and as a nationally important nature reserve for migratory birds in China. In this study, surface water, groundwater and wetland water were collected for the measurement of environmental isotopes to reveal the seasonal variability of oxygen and hydrogen isotopes (δ18O, δD), sources of water, and groundwater inflow fluxes. Results showed that surface water and groundwater are of meteoric origin. The isotopes in samples of wetland water were well mixed vertically in seasons of both high-flow (September) and low-flow (April); however, marked seasonal and spatial variations were observed. During the high-flow season, the isotopic composition in surface wetland water varied from −97.13 to −41.73‰ for δD and from −13.17 to −4.70‰ for δ18O. The composition of stable isotopes in the eastern region of this wetland was lower than in the western region. These may have been influenced by uneven evaporation caused by the distribution of aquatic vegetation. During the low-flow season, δD and δ18O in the more open water with dead aquatic vegetation ranged from −37.11 to −11.77‰, and from −4.25 to −0.08‰, respectively. This may result from high evaporation rates in this season with the lowest atmospheric humidity. Groundwater fluxes were calculated by mass transfer and isotope mass balance approaches, suggesting that the water sources of the Caohai Wetland were mainly from groundwater in the high-flow season, while the groundwater has a smaller contribution to wetland water during the low-flow season.