The invention discloses a regional water environment heavy metal monitoring system and an operating method. The regional water environment heavy metal monitoring system comprises a monitoring management system and a plurality of monitoring terminals, wherein the monitoring terminals are connected with the monitoring management system through general packet radio service (GPRS); a central processing unit of the monitoring management system is connected with a data transmitting and receiving module, a data analysis processing module, a database management module and a display or a user terminal; the data transmitting and receiving module is connected with a database storing global positioning system (GPS) information, information geographic information system (GIS) and correlated heavy metal concentration information detected by all the monitoring terminals; a master control module of each monitoring terminal comprises an embedded processor, a clock and a GPRS sub-module; a detection module comprises a temperature sensor and a heavy metal electrochemical sensor array. According to the operating method, the temperature and the heavy metal concentration, monitored by the monitoring terminals, of a water environment are transmitted to the monitoring management system to be stored and displayed, and are compared with standard values and historical data through the data analysis processing module; when the polluted water quality is determined or the concentration of certain heavy metal is suddenly increased to a higher level, an alarm is given. According to the regional water environment heavy metal monitoring system and the operating method, the pollution of a water body is timely found by real-time sampling analysis and dynamic monitoring; the monitoring terminals are simple to network and easy to expand.