The correlation between the δ13C and δ18O in primary carbonates is affected by several factors such as hydrological balance, total CO2 concentrations, climatic condition and lake productivity. The influence of these factors on the δ13C-δ18O correlation may be different on different time scales. In this paper, two different-type lakes in southwestern China, Lake Erhai and Lake Chenghai, are selected to investigate the influence of climatic pattern on the δ13C-δ18O correlation and to evaluate the reliability of the δ13C-δ18O covariance as an indicator of hydrological closure. The results show that there exists good correlation between the δ13C and δ18O in Lake Erhai (overflowing open lake) and in Lake Chenghai (closed lake). This suggests that the δ13C-δ18O covariance may be not an effective indicator of hydrological closure for lakes, especially on short time scales. On the one hand, a hydrologically open lake may display covariant δ13C and δ18O as a result of climatic influence. The particular alternate warm-dry and cold-wet climatic pattern in southwestern China may be the principal cause of the δ13C-δ18O covariance in Lake Erhai and Lake Chenghai. On the other hand, a hydrologically closed lake unnecessarily displays covariant trends between δ13C and δ18O because of the buffering effect of high CO2 concentration on the δ13C shift in hyper-alkaline lakes. We should be prudent when we use the covariance between δ13C and δ18O to judge the hydrological closure of lake.