Natural swimming pools are artificially created bodies of water that are intended for human recreational bathing and have no chemical disinfection treatment. The microbial populations in four private natural swimming pools were analysed to assess the typical microbiological parameters, establish the origin of faecal contamination in the water, and predict the behaviour of larger systems that are open to the public. For this purpose, faecal coliforms, E. coli, enterococci, aerobic heterotrophic bacteria and Pseudomonas aeruginosa were enumerated in summer and winter. Moreover, faecal coliforms and enterococci populations were biochemically phenotyped with the Phene-Plate System, the diversity and similarity indexes were calculated and the isolates were identified. Three of the four natural pools exceeded the E. coli or enterococci limits stated in the recommendations for natural swimming pools. The concentrations of P. aeruginosa and aerobic heterotrophic bacteria were acceptable. The results suggest that wildlife was an important source of faecal pollution in the pools. Since there is a lack of regulations on these systems, and the health risks are higher than in conventional swimming pools, further research is needed to establish the parameters for ensuring safe bathing in private and public natural swimming pools.