The estuary of the Loukkos River is a complex ecosystem where various factors affect the quality of water. Our study is assessing the degree of water pollution in the complex of the lower Loukkos wetland’s surface water, which is situated at the river mouth of the Loukkos river in the eastern periphery of Larache city. To realize this objective, we collected water samplings from five area sites during summer period from May to August 2016 to analyse eight parameters physicochemical including dissolved oxygen (DO), temperature, pH, electrical conductivity, turbidity, salinity, suspended matter and nitrates. This study was accompanied by a bacteriological analysis relating to the enumeration of total coliforms and faecal coliforms, intestinal enterococci and reducing anaerobic sulphites. The analysis’s results shed lights on factors of contamination and collaborate to the physicochemical evaluation and bacteriologic quality of surface water. The quality indicators spatialization reveals interactions between the various phenomena acting on the functions of this Ramsar site.