The invention discloses a method and system for tracing a regional water environment based on a river network mathematical model, and the method comprises the following steps: S1, obtaining the pollution condition of a monitoring point through an instrument, and transmitting the pollution condition into a database; S2, by patrol personnel, patrolling the river monitoring points, uploading patrol daily reports and storing the patrol daily reports in the database; S3, calculating the possibility of each monitoring point as a pollution source according to the real-time acquired data; S4, planning regular manual detection according to the result of a risk estimation module; and S5, when sudden water pollution occurs, estimating the possibility that each monitoring point is used as a pollution source, and preferentially checking the monitoring points with relatively high historical pollution occurrence probability. The system mainly comprises a risk estimation module, a regular manual detection module, an emergency scheduling module and a database. The method solves the problems of long time consumption and high difficulty in the water environment pollution tracing link, and has the advantages of quick tracing and real-time monitoring.