Urban surface water runoff typically contains a high but variable number of pathogens, nutrients, and sediments that require removal before reuse. Permeable pavements can improve the water quality through interception, filtration, sedimentation, nutrient transformation, and microbial removal. There is currently insufficient scientific information available on the treatment efficiencies of permeable pavements combined with earth energy systems with regards to the removal of storm water pollutants such as nutrients, sediments, and microbial pollutants. This study evaluates the efficiency of 12 tanked combined systems during a medium-term study. The research assessed weekly the removal of the microbial indicators total coliforms, Escherichia coli, and fecal Streptococci, as well as the key nutrients ammonia-nitrogen, nitrate-nitrogen, and ortho-phosphate-phosphorus, and physical variables such as suspended solids and turbidity. Total coliforms, E. coli, and fecal Streptococci were removed by 98–99%. The ammonia-nitrogen and ortho-phosphate-phosphorus removal efficiencies were 84.6% and 77.5%, respectively. An analysis of variance indicated that the presence or absence of a geotextile did result in a very highly statistically significant difference (P <0.001) with respect to the removal of both ammonia-nitrogen and ortho-phosphate-phosphorus. Suspended solids, turbidity, and biochemical oxygen demand were reduced by 91%, 82%, and 88%, respectively. These results indicate the potential of the proposed novel system in urban runoff pollutant removal and subsequent reuse of the treated water.