The PhD thesis focuses on the performance assessment of permeable pavement systems incorporating ground source heat pumps (GSHP). The relatively high variability of temperature in these systems allows for the survival of pathogenic organisms within the sub‐base. Salmonella sp, Escherichia coli, Enterococci and total heterotrophic bacteria were analysed in order to assess potential risk to health. Supplementary carbon dioxide monitoring indicated relatively high microbial activity on the geotextile and within the lower parts of the sub‐base. Anaerobic processes were concentrated in the space around the geotextile, where carbon dioxide concentrations reached up to 2000 ppm. The overall water treatment potential was high, with up to 99% biochemical oxygen demand removal. Variable removal efficiencies have been calculated for nutrients such as ortho‐phosphate‐phosphorus, ammonia and nitrates/nitrites. Calculated Coefficients of Performance and Energy Efficiency Rates provided evidence on correctness of GSHP design. Collected data was analysed with non‐parametrical statistics and a self‐organizing map model was used to assess relationships between variables. Findings present correlations considered as low and insignificant between temperature fluctuations and pathogen numbers. Highly significant correlations (p<0.01) were calculated for influent‐effluent relationships. Air and water temperatures and water quality data variability within the systems provided evidence for the high level of biological processes leading to a low risk of pathogen transition to human.