Vjosa is the main river of South Albania. Currently, the confined Quaternary gravelly aquifer in its lower course supplies drinking water for roughly 300,000 local residents. In the past years, extracted groundwater quantity has increased, whereas the groundwater quality has been affected by seawater intrusion. This paper aims to assess the groundwater quality and to discuss the dominant hydrochemical processes in the aquifer. To fulfil this goal, the study discusses the groundwater quality’s spatial and temporal variations on the basis of the hydrochemical parameters and ratios for 2010–2021 period, during which data are collected from three monitoring wells, located 6, 14 and 17 km, from the sea. While for 1961–2009 period, hydro-chemical water types and TDS maps are prepared using roughly 100 chemical analyses. The hydro-chemical parameters are discussed related to the factors controlling the groundwater’s chemical constituents and the groundwater extraction. Heavy metals and nitrates’ contents indicate that the aquifer is not affected by anthropogenic pollution. The main conclusion is that the groundwater quality is affected by seawater intrusion due to overexploitation. The study reveals its gaps, mentions its possible usefulness, and underlines the discrepancy between the policy makers and the hydrogeologists approaches concerning groundwater extraction.