The invention discloses a river habitat survey method and system. The method is applied to the river habitat survey system. The method comprises the following steps of A, fixing a device; B, detectingdata; and C, displaying the data. The system comprises a monitoring device, a server and an intelligent terminal, the monitoring device comprises fish and a detection device, the detection device isfixed to the surface of the fish body and is used for detecting the water quality data at the position of the fish, and the server is used for storing real-time water quality data of the position where the fish is located, analyzing the pollution degree at the position where the fish is located of the water body according to the water quality data of the position where the fish is located and sending the analysis result to the intelligent terminal.