Abstract Conducting a health assessment of rivers and lakes is a technical approach that enables the accurate diagnosis of water health status and scientific analysis of aquatic ecological environments. This paper focuses on studying the typical rain-sourced water bodies of Huangrigang River and Dishui Lake (DSL) in Lin-gang, Shanghai. The Australian Stream Condition Index and the Analytic Hierarchy Process were used to establish a typical river and lake health evaluation index system. Expert scoring and least-squares methods were used to determine the weights of each index, and a quartile method was used to establish the evaluation criteria. The evaluation results indicate that the health status of the Huangrigang River is sub-healthy with a score of 72.1, whereas DSL is healthy with a score of 75.7. The low flow velocity of the regional river and the weak mobility of the water body are the main issues affecting the health status of the HRGR. Additionally, the density of phytoplankton in the river is significantly high. Dripping Lake is faced with two major problems: a high risk of eutrophication and a high density of phytoplankton in the lake. This article provides theoretical support for the sustainable use of regional water resource.