Radon-in-water is an important tracer in hydrology, oceanography and geology, where a demand for fast response and long-term continuous measurement of radon-in-water concentration on-site is necessary. In this paper, an on-site radon-in-water measurement system based on a degassing membrane, an electrostatic radon monitor and a water temperature sensor is presented, and calibration experiment is carried out. The relative degassing efficiency of the degassing membrane was studied using self-made radon-in-water standard, which gives the result of (97.1 ± 7.3) %. The sensitivity of the measurement system is (3730 ± 190) cph/(Bq/L), and the lower limit of detection is 0.005 Bq/L, with 10 min cycle at 25 °C water temperature. The response time of the measurement system is about 26 min, which is independent of the water flowrate within the range of 0.5–2.5 L/min. Using this measurement system, field measurements were carried out on tap water and deep well water. And the measurement system has been successfully used in the continuous monitoring of radon-in-water concentration at a seismic station in Beijing.