The application of an in-situ gamma-ray spectrometer for long-term measurements of natural radionuclides into groundwater emanating from submarine groundwater discharge (SGD) sources is described. The system (named KATERINA) has been developed for aquatic applications by Hellenic Centre for Marine Research and as a preliminary study it was deployed at three pilot SGD sites in Greece. After the initial deployment into the lake Tsivlou where background spectrum was obtained, the system was deployed for several hours in Hellenic coastal submarine groundwater sources at Chalkida, Stoupa and Korfos. The radon progenies activity concentration at Chalkida measured in a range from 1.2 to 1.3 Bq/L while at Stoupa from 2.4 to 2.6 Bq/L. Also, the concentration of the radon progenies in the region of Korfos varied from 1.4 to 2.3 Bq/L and an inversely linear dependency with salinity values was observed. The system monitoring radon progeny variations may contribute to hydrological studies concerning the transport, the emanation and the quantification of the groundwater using radiotracing techniques.