This study assesses the impact of municipal and industrial wastewaters on the aquatorium of the northern port of the town of Rovinj. For this purpose, sanitary control of seawater and the distribution of microorganisms were carried out throughout the entire area of Valdibora Bay. Sampling of the water column was performed during June 2014 on a network of 13 stations. The conditions of the water at the reference stations, which were not under the direct influence of sewage pollution, were compared to the areas affected by wastewaters. The sanitary quality of the seawater was unsatisfactory near the outfall of the hospital complex and, in some cases, near the old town market. The most critical conditions were recorded in the part of Valdibora Bay exposed to the effects of the fish processing factory outfall, where the concentrations of faecal indicators were comparable to those recorded around the main sewage outfall of Rovinj. The number of heterotrophic nanoflagellates and cyanobacteria was relatively low, while the number of heterotrophic bacteria around the outfall of the fish cannery exceeded the limits of naturally-occurring variations for the coastal waters of Rovinj. The salinity and temperature values in the water column of Valdibora Bay were typical for the east coast of the North Adriatic. The lowest concentrations of oxygen were recorded in the area around the outfall of the fish cannery due to the influx of organic matter and its degradation in the sea while the oxygen saturation in the rest of the bay was relatively high.