A recent innovation in air phytoremediation is active green walls, which utilises biofiltration technology with airflow from mechanical ventilation. While this novel technology is gaining traction, the influence of irrigation on soil moisture, and subsequently the microbial communities that play a role in air filtration is untested. In this study, the application of drip irrigation techniques in active green walls were investigated for their influence on system performance. A modular green wall system was tested, with tests across 7 different plant species, as well as a substrate only control. Water distribution across the modules, the water-carrying capacity and airflow through the substrate were measured. The microbial community present, which is critical to the phytoremediation process, was quantified by identifying individual microbial phospholipid fatty acids (PLFA) within the substrate. Results demonstrated that the lower-speed drip irrigation reduced water consumption compared to the rapid system, and had generally more uniform moisture distribution. High flow drip irrigation resulted in a water pathway phenomenon, leading to uneven moisture distribution within the green wall, and this effect was accentuated with fibrous root plant species. Drip irrigation did not change microbial community composition across planted modules, apart from increasing fungi by 6%, but did wash out bacteria at the high flow rate used (−56.67%), thus low flow rate irrigation rate is more beneficial for both plant growth and microbial community composition. The current work provides evidence that drip irrigation has considerable effects on both substrate airflow rate and substrate microbial density: both key to system air cleaning performance.