A protozoological survey was done to isolate free-living amoebae from swimming pools and physiotherapy tubs in Mexico City. Amoebae were isolated by culture in nonnutritive agar medium combined with Escherichia coli. Identification of the isolates was done by morphology using specialized taxonomic keys and by isoelectric focusing of total proteins and isoenzymes in agarose. Pathogenicity of the isolates was determined in 3-week-old mice by intracerebral and intranasal inoculations. Statistical tools were used to determine the existence of significant differences on the incidence and diversity of the isolates in relation to the two types of water bodies analyzed. Water and environmental temperatures, pH, and chloride concentrations were determined at each sampling site. Twenty-nine amoebic strains from eight genera were isolated. Most frequently found were specimens of the genera (Acanthamoeba (with four pathogenic strains), Vahlkampfia, Hartmannella, and Naegleria. Amoebae were isolated more frequently in spring and summer, and could not be recovered from pools with chloride levels of 5.31 mg/ml or more. This survey demonstrates that chloride concentrations commonly used in recreative pools and therapy tubs are not sufficient to eliminate viable cysts of most free-living amoebae. Significantly higher numbers of isolates were retrieved from the pools than from the tubs.