The potential of an express enzymological indicator – phosphatase activity index (PAI) – for assessment of different types of pollution and self-purification potential in running waters was evaluated for three river subcatchments, representative for different ecological situations and impacts. According to the values of correlation coefficients, a significant positive correlation existed among PAI and total microbial count, organic loading and phosphate concentrations. The enzyme activity is useful tool for early identification of risks from point discharge of different wastewaters (treated or non-treated). The role of PAI as an indicator is significant at case of disinfection after treatment of wastewaters in treatment plant – the aquatic microbial community at the discharge point is suppressed but not at a functional level. The results allow classical microbiological and chemical parameters (state variables) to be related directly to the dynamics of the transformation processes by functional variable – PAI.