Key ecological processes must be present and maintained in ecosystems to ensure the success of ecological restoration and conservation programs. The present paper identifies and defines key ecological processes operating at various spatial scales within aquatic ecosystems of the Magela Creek catchment, within Kakadu National Park, and prioritises those that may be vulnerable to potential mine-derived stressors. This assessment was required to ensure that current and future environmental monitoring programs are in place to safeguard the protection of these processes, particularly in the context of rehabilitation of Ranger uranium mine. Ecological processes within riparian habitats and biotic interactions across all habitats were at a higher risk of exposure to potential stressors. Generally, the selected assessment endpoints used for the operational phase of the mine are sufficient to measure and assess ecological processes. However, biological endpoints require additional suitable early detection indicators because marked lags exist in their response, which will be more important during the rehabilitation phase of the mine because of the longer timeframes to be assessed. The lags would otherwise allow potential impacts to underpinning processes to pass undetected. Risk identification allows monitoring programs to move beyond simple measurement variables to full evaluation of underlying ecological processes, which maintain both structure and function in ecosystems.