Possible transmission pathways of fungi in indoor swimming pool facilities were assessed through fungal counting in different areas of the facilities and typing of the collected fungal isolates. Air, water and surface samples were collected from seven different indoor swimming pool facilities. Fungal species were identified based on their internal transcribed spacer (ITS) sequences. Maximum fungal concentrations of 6.2 CFU/cm2, 1.39 CFU/100 mL, and 202 CFU/m³ were found on surfaces, in water and air, respectively. In total, 458 isolates were obtained, belonging to 111 fungal species, of which 50 species were clinically relevant. Phialophora oxyspora (13.3%) and Trichosporon dohaense (5.0%) were the most frequently isolated species and were merely detected on floors, as were the dermatophytes, Trichophyton interdigitale and T. rubrum. Penicillium spp. and Aspergillusspp. were the dominant fungi in water and air. No typical patterns of fungal concentrations along the preferential pathways of pool visitors were observed, however, sites where pool visitors converge while moving from one room (e.g. dressing room) to another (e.g. shower room) and walking barefoot displayed the highest fungal concentrations thus posing the highest risk of contamination. The dispersal of fungi on floors is most likely facilitated by the pool visitors and cleaning tools. Clinically relevant fungi, including the ones rarely identified in nature, were widely detected on floors, in water and in air, as well as on cleaning tools and flexibeams. Preventive measures such as cleaning should minimize the prevalence of clinically relevant fungi in swimming pool facilities since these potentially pose health risks to those vulnerable for infections.