Green infrastructure (GI) stormwater control measures (SCMs), such as permeable pavement systems, are common practices used for controlling stormwater runoff. In this paper, two permeable pavement strips were studied to quantify their water quality performance. The quality monitoring was coupled with comprehensive rainfall analysis to investigate the effects of common rainfall characteristics on the quality performance of the systems. The pavements utilized deep aggregate layers to promote higher infiltration, and were installed in parking lanes of an urban neighborhood. Water quality samples were collected from upgradient stormwater runoff and from stormwater captured by the permeable pavements. In addition to total suspended solids (TSS), nutrients, and dissolved metals, this research also investigated bacterial contamination (Escherichia coli, E. coli). The results indicated that the two permeable pavement systems significantly reduced concentrations of TSS, E. coli, total phosphorus, and ammonia. The average reductions of TSS and E. coli between the two systems were 47% and 69%, respectively. It was also observed that pollutant loadings in the stormwater runoff, as well as pollutant reductions, were affected by the intensity of sampled rainfall events. Thus, it is suggested to consider the effects of rainfall characteristics when reporting the water quality benefits of stormwater GIs.