Seawater contains numerous allochthonous microorganisms that can pose a direct danger to human health. Therefore, it is important to monitor the quality of coastal recreational waters. Special attention is given to microorganisms that thrive in the human digestive tract, namely Escherichia coli and intestinal enterococci, which are also used to assess the microbiological quality of seawater. Environmental factors such as temperature, pH, salinity, solar radiation and precipitation can impact the concentration of indicator microorganisms, but the impact of precipitation on the concentration of indicator microorganisms has been less investigated. In addition to the influence of precipitation, this paper also questions the possibility of using Staphylococcus aureus as an additional parameter for assessing seawater quality. Sampling was performed at eleven stations in the Trogir, Kaštela bay and Split area, and the control station was situated away from populated areas. The results showed that lower amounts of precipitation do not affect the concentration of indicator microorganisms. It has also been shown that S. aureus could be further investigated to serve as a parameter for assessing seawater quality.