The present study was undertaken in order to determine the quality of indoor pool waters in hotels along the Croatian coast. We wanted to assess the risks of exposure to microbial and chemical contaminants and find out if training pool operators to use a quality assurance system, that we developed, influenced hygienic conditions and water quality in swimming pools or not. The samples were analysed for free chlorine, pH and several microbiological indicators according to standard laboratory methodologies. Of 1,329 samples tested, 276 were found to be unacceptable either by chemical (148) or microbiological parameters (128). After training, the proportion of unacceptable samples dropped by 23.5%, mostly according to the free chlorine values. According to our results, most of the microbiologically unacceptable samples had chlorine levels within the recommended range but their pH values were too high. A free chlorine level below 0.2 mg/L was found in 106 (82.8%) microbiologically unacceptable samples suggesting the need for maintaining the lower limit at least above 0.2 mg/L in order to reduce microbial risks to a more acceptable level. This measure combined with training of pool operators might result in reduced health risks in pool waters.