The waters renewal of the fishery harbor of Nea Krini is presented here. The harbor is located at the east Thessaloniki Gulf (NE Thermaikos Gulf, Greece). The main research point is focused on the environmental state of the harbor which is under construction. Under that point of view, the description of a two-dimensional, depth average, hydrodynamic model follows, in order to simulate the wind generated circulation of waters, initially on the greater area of Thermaikos Gulf and then on the coastal basin of the fishing harbor. The renewal of waters in the harbor's basin is subsequently studied. Tidal effects on the waters' renewal are also studied. The calculation of the concentration of Biochemically Oxygen Demand (BOD) in the fishing harbor for the average time of waters' renewal is then examined for three different cases, concerning the existence and operation of openings on the body of the groins. Finally, the analysis of the results shows a good environmental state of the harbor. It is obvious that the use of numerical models for different scenarios of engineering and design approaches can lead to the prognosis of hydrodynamic and environmental sate of a harbor's basin so that the best possible technical design can be adopted.