Obtaining reliable estimates of vertical groundwater flows remains a challenge but is of critical importance to the management of groundwater resources. When large scale land clearing or groundwater extraction occurs, methods based on water table fluctuations or water chemistry are unreliable. As an alternative, a number of methods based on temperature-depth (T-z) profiles are available to provide vertical groundwater flow estimates from which recharge rates may be calculated. However, methods that invoke steady state assumptions have been shown to be inappropriate for sites that have experienced land surface warming. Analytical solutions that account for surface warming are available, but they typically include unrealistic or restrictive assumptions (e.g. no flow initial conditions or linear surface warming). Here, we use a new analytical solution and associated computer program (FAST) that provides flexible initial and boundary conditions to estimate fluxes using T-z profiles from the Willunga Super Science Site, a complex, but densely instrumented groundwater catchment in South Australia. T-z profiles from seven wells (ranging from high elevation to near sea level) were utilised, in addition to mean annual air temperatures at nearby weather stations to estimate boundary conditions, and thermal properties were estimated from down borehole geophysics. Temperature based flux estimates were 5 to 23 mm y− 1, which are similar to those estimated using chloride mass balance. This study illustrates that T-z profiles can be studied to estimate recharge in environments where more commonly applied methods fail.