Legionella bacteria living in free form or in biofilm and free-living amoebae (FLA) can infect humans through swimming pools and can cause various diseases. FLA may also threaten the health of swimmers because they are capable of being hosts for Legionella and some other bacteria. The aim of this study was to investigate the presence of total aerobic heterotrophic bacteria (TAHB), FLA and Legionella bacteria in swimming pool waters and biofilm samples in Istanbul by using culture and FISH methods. Water plate count agar (wPCA), buffered charcoal yeast extract (BCYE) agar supplemented with glycine-vancomycin-polymyxin-cycloheximide (GVPC) and Escherichia coli cultivated non-nutrient agar (NNA) were used for the culture of TAHB, Legionella and FLA. For the FISH method analysis, Leg 705 and Leg PNE1 probes labeled with fluorescent dye for Legionella and ACANTHA probe for Acanthamoeba genus FLA were used. Legionella pneumophila serogroup 1 ATCC 33152, L.pneumophila serogroup 3 ATCC 33155 and Acanthamoeba castellani ATCC 50373 were used as positive controls. TAHB were grown in 92% and 84% of water and biofilm samples. Although Legionella bacteria could not be grown in any of the water samples, it was detected in 6 (24%) water samples by FISH method. Although these bacteria could be grown in 1 (4%) of biofilm samples, 7 (28%) were detected by FISH method. FLA were found to be 16% by culture in water samples and 28% by FISH analysis. These amoebae were detected 8% and 20% in biofilm samples by culture and FISH method, respectively. It was determined that one of the isolates of FLA had thermotolerant activity (potentially pathogenic). L.pneumophila serogroup 1 was detected in one water sample and in four biofilm samples. According to the culture method, TAHB and FLA were found to be more common in water samples than in biofilm samples and Legionella bacteria were more common in biofilm samples than in water samples (p <= 0.05). In the detection of Legionella bacteria, the superiority of FISH method compared to culture method was found to be statistically significant (p <= 0.05). In this study, it was found that the number of TAHB in the controlled swimming pools was within the limits determined by the Ministry of Health (<= 200 cfu/ml). It will be appropriate to examine both water and biofilm samples for the investigation of TAHB, FLA and Legionella. It may be appropriate to use both culture and FISH methods to detect the presence of FLA in water and biofilm samples. This study is the first study to investigate the presence of Legionella and FLA in swimming pools in Istanbul, and further studies are needed to examine more pool water and biofilm samples. With the data obtained, the health principles and controls of swimming pools will be re-considered and will be contributed to public health.