The Buna River-Protected Landscape is a Managed Nature Reserve and Ramsar site because of its high biodiversity; the water resources at this site represent a crucial element for the ecosystem conservation, especially for the avifauna and ichthyofauna. Water-quality assessment and monitoring are important to the water resource’s ecological value and the health of local populations to improve and promote sustainable agriculture and ecotourism. This paper reports a hydrogeochemical evaluation of sampled waters from the Buna River-Protected Landscape in northern Albania. There exist no previous studies that assess the environmental status of the local groundwater resources. Geochemical surveys of groundwater were conducted in October 2012, and February and June 2013 within the framework of the “International Union of Conservation of Nature”, granted by the Italian Ministry of Foreign Affairs. Twenty samples were analysed to (1) study several parameters with respect to 2000/60/EC and 2006/118/EC, which pose risk for environmental health and (2) evaluate the water quality and all processes that can influence it. The sampled groundwater was classified as calcium bicarbonate, and no evidence of saline intrusion phenomena was obtained, even in the area closest to the coast. Areas with a greater anthropogenic presence show NO3 levels above the European Union thresholds, probably due to the lack of wastewater management systems. A major concern is represented by the widespread presence of organochlorine pesticides, especially with reference to the Hexachlorocyclohexane isomers that have concentrations widely above the thresholds suggested by the European Union