Enzyme activity plays an important role in the functioning of aquatic ecosystems. It is sensitive to changes in environmental conditions such as pH, temperature, and nutrient concentration. The objective of this work was to determine the acid phosphatase activity (AcPA) in the Almendares and San Juan rivers (western Cuba) and its relationship with physicochemical and microbiological indicators. For this purpose, AcPA, temperature, pH, total dissolved solids, electrical conductivity, dissolved oxygen, concentration of nitrates, nitrites, ammonium, phosphates, total heterotrophs, enterococci, Escherichia coli, thermotolerant coliforms, chlorophyll a and chemical oxygen demand (COD) were determined at three sampling stations on the Almendares River and at three sampling stations on the San Juan River. In addition, the nutrient pollution index (NPI) and the N:P ratio were calculated. In both ecosystems, spatio-temporal variability was observed in the enzymatic activity. In the Almendares River (polluted ecosystem), AcPA was positively correlated with nitrate concentration and COD. While in the San Juan River (slightly contaminated ecosystem) the AcPA correlated negatively with the pH and NPI and positively with the concentrations of total heterotrophs, Escherichia coli, chlorophyll a and the N:P ratio. These results show the impact of anthropogenic pollution on AcPA in freshwater ecosystems with a tropical climate.