A declining population of the freshwater turtle Mauremys rivulata (Chelonia, Geoemydidae) living in a human-impacted area along the Strymon River, just upstream from Kerkini Lake (Prefecture of Serres, northern Greece), was investigated by capture–recapture and radio-tracking. Fyke nets placed along the river and in ponds lying on the riparian lowland gave about 2000 catches in 6 years, permitting us to assess major inter-habitat movements during ontogenesis and throughout the seasons. Annual intensive radio-tracking of 15 females and 10 males gave finer details of movement patterns between different river-wetland habitats. Younger specimens, including yearlings, inhabited the ponds almost exclusively, whereas the adult population shifted seasonally from the ponds during the mating season to a marsh area lying on the opposite side of the river for aestivation and overwintering. The river served mainly as a corridor for transit between the two habitats. Moreover, longitudinal movements along the river were observed, particularly in the males, which probably allow dispersal and gene flow between subpopulations living in the area. One major threat to the viability of M. rivulata in the study area is the diversion of water for irrigation during the summer, drying up the Strymon completely, which reduces the water level in the ponds. Livestock crossing the area for grazing and watering in the ponds is also of impact, as turtles in the ponds are trampled on and nests are disturbed.