The invention discloses an automatic detection method for a pollution source in a water area, and the method employs a controller, a drive unit, a sampling device, an azimuth sensor and water quality sensors, wherein the drive unit, the sampling device, the azimuth sensor and the water quality sensors are controlled by the controller. The method comprises the steps: (1), setting a contaminant detection threshold value S0; (2), enabling the plurality of water quality sensors to collect the pollutant concentration simultaneously at the time interval delta T, and comparing the maximum value S of the data with S0: enabling a detection device to continue to move forward in an initial direction when S is not greater than S0, or else, enabling the detection device to move forward in a direction of the water quality sensor corresponding to the maximum value S till to reach the area where the pollution source is located. The method can carry out automatic cruising, automatic positioning and unmanned operation in the water region, can automatically search the position of the pollution source in the water area, and can bring back a sample. The method can reach a water region which cannot be reached by a person, or a water region with a big danger. The method can automatically monitor the condition of the water quality of a large-area water area in real time, and obtains the specific pollutant concentration of the water area.