Determining variations in groundwater replenishment over a variety of time scales remains a challenge in the management and protection of groundwater resources. Specifically, capacity to use hydraulic data collected in small windows of time to infer long-term changes can be limited by system responses. Groundwater ages offer an alternative approach as they represent the time since recharge occurred. Here we use spatial variations in groundwater ages and environmental tracer concentrations to infer temporal variations in groundwater recharge and apply the method to a mine site in northwest Australia, where a stream has been modified from ephemeral to perennial, resulting in enhanced recharge to groundwater. Measurements of 14C and CFC-12 at five transects along an ephemeral stream were interpreted with the new model to identify recharge rates and the proportion of recharge attributable to enhanced versus natural recharge from flood events. Enhanced recharge varied between 0.03 and 0.66 m/year compared to flood-generated recharge values ranging between 0.07 and 1.3 m/year. Our results show that spatial variations of groundwater ages and environmental tracer concentrations preserve information about past flow regimes. While our study has demonstrated decadal variations in recharge, application of the method on larger scales could infer much greater extent of temporal variability in recharge, with the potential for significant insight into climate effects on groundwater.