Abstract: Reservoir operations can cause spatiotemporal changes in downstream water quantity and quality, leading to negative impacts on the dynamics of aquatic community systems (ACS). To explore the propagation and accumulation effects of stochastic disturbances in water quantity and quality within ACS, and to improve the stability of ACS downstream of reservoirs, this study proposed a system stability evaluation index called the “cumulative ratio” by establishing a stochastic dynamic system model. Multiobjective optimization operations were performed taking the Danjiangkou Reservoir and the middle–lower reaches of the Hanjiang River (China) as the study area. Results revealed substantial variations in the propagation of uncertainty coefficients of different water quantity and quality indicators within the ACS. The ACS of upstream stations exhibited greater stability under environmental disturbances compared with those of downstream stations. The average annual water supply and average annual hydropower generation of the optimized scheme were enhanced by 4.32% and 0.26%, respectively, compared with those of the conventional operation scheme. The stability of ACS at multiple downstream stations was improved by an average of 1.58%. These findings provide valuable technical support for water resource management and ecological governance.