The invention relates to a device for online monitoring the CO2 excretion rate of aquatic organisms in real time and a water environment monitoring method. The device comprises a respiratory chamber,a three-way valve, a fluid-flow pump, a digital controller, an environment signal detecting device, a CO2 concentration detecting device, a data collector, and a computer. In order to improve the precision of measurement, a gas-liquid separator, a silica gel drying tube, and a polytetrafluoroethylene filter are arranged, the gas in water is separated and dried before the CO2 concentration measurement, and the provided device can realize real-time online long-term monitoring. At the same time, the invention provides a method of using the provided device to monitor water environment. The indexessuch as CO2 concentration, atmospheric pressure, temperature, salinity, and the like, are collected, the detected data is processed to obtain the CO2 excretion rate of aquatic organisms, and the water environment is monitored.