Aquifers are increasingly stressed. Managed aquifer recharge provides a potential solution to mitigate this stress and provide sustainable groundwater resources. Subsurface properties are known to have a strong control on the infiltration rates that can be achieved. However, these properties are often highly heterogeneous and difficult to assess with conventional probing techniques. Here, we show the application of 3D geophysical imaging to assess the recharge potential and its variation across several basins used for managed aquifer recharge. We link in-situ measurements of saturated hydraulic conductivity with the electrical resistivity of the subsurface to establish petrophysical relationships and use those relationships to estimate the distribution of hydraulic conductivity throughout the five recharge basins. Our results show a considerable variability in the hydraulic properties, i.e., soil texture and saturated hydraulic conductivity, that have a direct impact on potential infiltration rates. We use the 3D hydraulic property distributions to model groundwater recharge and provide estimates for infiltration rates and volumes, and use this approach to assess the impact of management activities on groundwater recharge performance. Having such data not only enables us to predict infiltration rates, but also provides means for optimizing such water infrastructure.