Recharge processes in arid and semi-arid environments are characterised by their high variability both temporally and spatially, making it difficult to determine appropriate components of water balances. However, quantifying recharge and understanding how recharge volume responds to changes in climate and hydrological regimes underpins accurate prediction of long-term water supply and water level recovery. We used environmental tracer techniques (including stable isotopes, radioisotopes, and anthropogenic compounds) to estimate ephemeral stream recharge processes in the Pilbara region of northwest Australia. We interpreted soil water profiles (> 6 m depth) of stable isotopes with a model of groundwater flow to assess recharge mechanisms and evapotranspiration in the riparian corridor of an ephemeral stream. We also used CFC-12 and 14C data coupled with a simple flow and groundwater-age model to investigate the change in groundwater recharge over time, with an emphasis on how the modified stream flow regime due to mining water discharge over the previous 10 years had altered groundwater recharge. The model applied an approach of correcting groundwater ages proportional to the flow rate in the system. We were able to identify that in upstream areas with (now) perennial surface flows, groundwater recharge was up to 200% greater than pre-mining conditions. At sites downstream where event-driven stream flow remains dominant, groundwater recharge was consistent with pre-mining conditions. Our results indicate that the spatial variation of groundwater ages is indicative of temporal variation in groundwater recharge. The scales of variability identified in our study, corresponded to the time scales of variability in recharge concentrations of the measured tracers. However, applying a similar methodology with tracers of “old” groundwater could give insight into variability of longer-term recharge.