Managed aquifer recharge (MAR) using treated effluent and stormwater (TES) as source water is a vital strategy for sustaining urban aquifers used for potable water supply in water-scarce regions. However, concerns exist about the adverse impacts on groundwater quality due to the introduction of emerging contaminants (ECs) typically present in TES. This study aims to assess the impact of MAR on groundwater quality in the Atlantis Aquifer by investigating the occurrence and spatial distribution of ECs, including pharmaceuticals, pesticides, and industrial chemicals. Twenty samples from MAR source water, groundwater, and surface water were collected and analysed for 289 ECs. Preliminary results showed the detection of 120 compounds, with MAR source water having the highest number of detections, followed by MAR-impacted groundwater, while naturally recharged groundwater had the fewest. This pattern suggests that ECs are introduced into the aquifer through MAR, that some ECs may be attenuated, and that there is a baseline level of contamination in naturally recharged groundwater. Further analysis involving a three-tiered health risk assessment revealed that fewer than 10% of detected compounds pose potential health risks (RQ >1). To assess the aquifer’s capacity to naturally attenuate (via biodegradation) ECs that pose potential health risks, conventional water quality indicators (e.g., nitrate, dissolved oxygen, manganese, sulphate) collected between 2018 and 2024 will be analysed. The findings will contribute to the development of an EC monitoring framework for the Atlantis Aquifer, and by integrating EC monitoring into existing management practices, this will enhance protection of both the resource and communities that depend on it.