Freshwater samples were physicochemicaly characterized to preliminary assess the ecological status of various aquatic habitats located in the region of Thrace. A range of physicochemical traits, such as pH, electrical conductivity (EC), cations like sodium, potassium, ammonium, lithium, magnesium and calcium, anions like nitrate, nitrite, fluoride, chloride, bromide, sulphate and phosphate, were determined. The organic content as estimated by COD measurements and the concentrations of certain heavy metals were also determined. The pH of the analyzed freshwater samples ranged within 7.54 to 7.97, which is typical for freshwater ecosystems. The EC was below 1 mS/cm in the majority of the analyzed samples, apart from those influenced by seawater, whose EC was determined as high as 23 mS/cm. In the freshwater samples with relatively high salinity, as expected, the anions and cations listed above were determined in increased concentrations. No ammonium and nitrite ions were detected in any sample examined, whereas, in the majority of the analyzed samples, PO43--P and NO3--N concentrations were below 0.2 and 1.5 mg/L, respectively. Heavy metals analyzed were either absent or detected at limited concentrations. Based on COD measurements, the organic content was low in most of the samples analyzed. Moreover, no phenolics were detected in the examined freshwater samples.