A changing climate and increasing urbanisation has driven interest in the use of aquifer storage and recovery (ASR) schemes as an environmental management tool to supplement conventional water resources. This study focuses on ASR with stormwater in a low permeability fractured rock aquifer and the selection of water treatment methods to prevent well clogging. In this study two different injection and recovery phases were trialed. In the first phase ∼1380 m3 of potable water was injected and recovered over four cycles. In the second phase ∼3300 m3 of treated stormwater was injected and ∼2410 m3 were subsequently recovered over three cycles. Due to the success of the potable water injection cycles, its water quality was used to set pre-treatment targets for harvested urban stormwater of ≤0.6 NTU turbidity, ≤1.7 mg/L dissolved organic carbon and ≤0.2 mg/L biodegradable dissolved organic carbon. A range of potential ASR pre-treatment options were subsequently evaluated resulting in the adoption of an ultrafiltration/granular activated carbon system to remove suspended solids and nutrients which cause physical and biological clogging. ASR cycle testing with potable water and treated stormwater demonstrated that urban stormwater containing variable turbidity (mean 5.5 NTU) and organic carbon (mean 8.3 mg/L) concentrations before treatment could be injected into a low transmissivity fractured rock aquifer and recovered for irrigation supplies. A small decline in permeability of the formation in the vicinity of the injection well was apparent even with high quality water that met turbidity and DOC but could not consistently achieve the BDOC criteria.