Monitoring quantity and quality data of a 3-yr (2006-2009) survey in the lower reach of Nestos river are presented. For the purposes of this study, monitoring was taking place at six sites along the river course. Discharge measurements were made at four stations. Physicochemical parameters (i.e., electrical conductivity, pH, dissolved oxygen and water temperature) were measured in situ while water quality samples were collected on a bi-weekly basis at all six stations along the river. Water samples for chemical analyses were collected for the determination of total phosphorus, orthophosphate, nitrite and nitrate nitrogen, ammonia, biochemical oxygen demand (BOD), chemical oxygen demand (COD), chlorophyll-a, TSS, alkalinity, sulfuric and chloride anions, major cations (Na(+), K(+), Mg(+), Ca(+)) and metals. Two autographic telemetric stations also provided continuous stage and water quality data at two of the sites. ANOVA and t-test statistical analysis were used for the interpretation of the collected data. Nutrient concentrations were found within acceptable limits, while bicarbonates were the dominant ions. No significant seasonal and spatial variations were observed, suggesting little impact from human activities on the part of river basin under investigation.