carbon (C), nitrogen (N) and phosphorus (P) are three of the most important elements for estimating ecosystem biogenic elements status and algal growth. Therefore, the C:N:P ecological stoichiometry serves as an important reference to guide water quality management and helps elucidate the aquatic ecosystems mechanism. This study firstly provides the information on the seasonal changes of dissolved organic matter (DOM) pool (dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and dissolved organic phosphorus (DOP)) under base-flow and rainfall-runoff scenarios, and then analyzes the optimal variation of C, N and P stoichiometry for freshwater ecosystem. Comparing the element contents under the two different scenarios, the results show that rainfall and runoff volumes are the major causes of the C: N: P ratios changes. We find out that the value of DOC is significantly higher than the value of DON and DOP. In addition, the DOC is the one of the major causes for trapping DOM, which accounts for 95% of the total DOM in freshwater ecosystem. And the change of DOP is the smallest as it compares to the changes of DOC and DON. It is discovered that the DOC: DON: DOP molar ratios in the watershed have an exponential distribution. The optimal DOC: DON: DOP ratio is 170–985:17–34:1 for the freshwater ecosystem. Moreover, the results suggest that the DTN: DTP (dissolved total nitrogen: dissolved organic phosphorus) ratio that equals to 10–64:1 will be the most beneficial for Xiangxi River basin in freshwater ecosystem. This result also indicates that the element of phytoplankton, which plays an important role in determining the trophic structures and community, is limited in the freshwater ecosystems.