During the last years, the report of the occurrence of waterborne disease symptoms related to non-enteric pathogens has increased, without any record of higher levels of indicator bacteria (Escherichia coli and intestinal enterococci). Therefore, the use of current indicators is not always adequate when assessing the overall potential health risk and the inclusion of additional parameters needs to be examined. This paper reports on the incidence and levels of Staphylococcus aureus at 258 locations in Primorje-Gorski Kotar County (Croatia) recorded by official bathing water quality monitoring, as well as supplemental monitoring carried out at the two most frequented beaches in the City of Rijeka. The number of bathers was found to be the main factor affecting S. aureus levels (r = 0.321, p < 0.05). The share of S. aureus positive samples from the official monitoring was significantly lower, when compared to the share of samples from supplemental monitoring (2.2% and 36.3%, respectively; p < 0.01). Besides the number of bathers, one of the main reasons is likely the higher sampling frequency. No correlation was found between S. aureus levels and the indicator bacteria. The results indicate that the determination of S. aureus and increased sampling frequency is recommended for overcrowded beaches.