The invention discloses a water quality monitoring system based on a Beidou navigation satellite system. The water quality monitoring system comprises a data collection ship, a data receiving node and a remote controller, wherein the data collection ship is used for collecting water quality parameters, and the data receiving node is arranged on the bank; a first control module as well as a water quality parameter collection module, a Beidou module, a compass module, a first wireless module, a paddle motor driving module and a display module which are respectively connected with the first control module are arranged on the data collection ship; the data receiving node comprises a second control module as well as a second wireless module and a warning device which are data collection ship connected with the second control module, and the second control module carries out wireless data transmission with the first wireless module; the remote controller carries out wireless control signal transmission with the first wireless module by virtue of a third wireless module. According to the water quality monitoring system, the water quality parameters are continuously collected by virtue of the data collection ship during cruising and are transmitted to the data receiving node by virtue of the wireless module, and the data collection ship can automatically cruise under the setting of the remote controller, so that the cost is low, and the automation level is high.