In order to investigate the water quality status of the cross section of Didonggou River to Jialing River, a one-dimensional unsteady flow model coupled with Thomas algorithm was constructed to study the current situation of water environment in Didonggou River based on in situ investigation, data collection and field synchronous monitoring. The results show that the main indicators that exceeded the required standards were NH3—N and TP; the proposed model exhibited excellent performance with high precision and reliable prediction results; the amount of NH3—N and TP pollution discharge to Jialing River were 43.1 t/a and 3.9 t/a, respectively; according to the analysis of the composition of pollution sources, about 76.5% of the pollution load was contributed by the urban sewage; from the spatial perspective, over 92% of the pollution load came from the upstream; the water environmental capacity of Didonggou River for NH3—N and TP are 16.3 t/a and 2.2 t/a, respectively. It is suggested that control measures such as repairing the sewage pipe network in the Didonggou River Basin, improving the rate of piped sewage and reducing pollution load should be implemented, so as to make the water quality of the Didonggou to Jialing River section reach the required standard.