In this paper, the sanitary and microbiological condition of the sea in the port of Valbandon is analyzed salinity and temperature at six locations within the port. The results of the sanitary quality of the sea in the winter period indicated mild pollution probably related to the intake of fresh water flowing into the artificially created salt marsh in the extension of the port. Concentration of indicators (FK, FS, E.coli) of sanitary quality of the sea precisely in the area of ​​the precipitation channel it is slightly elevated, but nevertheless the quality of the sea according to the standards for assessing the quality of the sea it was rated as excellent. On the other hand, in the summer the concentration of indicators was generally very low, with a slight increase again right next to the precipitation channel that brings in fresh water and whose yield given the much higher salinity in the summer months reduced, so it can be concluded that the source of mild pollution was precisely the inflow of fresh water. The ratio of fecal coliforms to fecal streptococci indicates that it is present at most stations fecal contamination of human origin, which may be related to nearby sewer drains, with soil leaching of the surrounding settlement and camp while in the summer are mostly animal fecal contaminants. The number of microbial communities was moderately above normal in some locations border indicating a higher degree of eutrophication within the port and wetland. Heterotrophic bacteria had the highest concentration with fresh water inflow in both sampling periods due to the probable influx of organic matter into the fresh water that serves them as food, which then leads to and heterotrophic nanoflagellates to an increase in numbers since they feed on heterotrophic bacteria. The general condition of the study area can be characterized as good, but due to the proximity potential sources of pollution, limited water circulation within the port and its shoals there is a risk of deterioration of the sanitary and microbiological condition and is therefore suggested regular monitoring of microbiological parameters in order to preserve the health of port users, bathers and the environment.