Biofilters have been shown to effectively treat stormwater and achieve nutrient load reduction targets. However, effluent concentrations of nitrogen and phosphorus typically exceed environmental targets for receiving water protection. This study investigates the role of filter media, vegetation and a saturated zone (SZ) in achieving co-optimised nitrogen and phosphorus removal in biofilters. Twenty biofilter columns were monitored over a 12-month period of dosing with semi-synthetic stormwater. The frequency of dosing was altered seasonally to examine the impact of hydrologic variability. Very good nutrient removal (90% total phosphorus, 89% total nitrogen) could be achieved by incorporating vegetation, an SZ and Skye sand, a naturally occurring iron-rich filter medium. This design maintained nutrient removal at or below water quality guideline concentrations throughout the experiment, demonstrating resilience to wetting–drying fluctuations. The results also highlighted the benefit of including an SZ to maintain treatment performance over extended dry periods. These findings represent progress towards designing biofilters which co-optimise nitrogen and phosphorus removal and comply with water quality guidelines.