Estimation of groundwater recharge rates (GRRs) in space and time is notoriously challenging but underpins water resource management. GRRs derived from different techniques often differ as they estimate different components (i.e., potential, net, gross) and/or estimate different GRR mechanisms (i.e., diffuse or focused). We evaluate GRRs from daily groundwater level data from ~400 bores across Australia using the water table fluctuation (WTF) method. Specific yield values are estimated using lithological information linked to literature values. Comparisons were made between mean inter-annual GRRs from 224 bores and long-term GRRs derived from the chloride mass balance (CMB) method. Mean inter-annual WTF-based GRRs were 365.5 mm/y for humid, 248 mm/y for dry subhumid, 128.6 mm/y for semi-arid and 50.3 mm/y for arid zones. Inter-annual recharge variability is higher in arid and semi-arid climate zones relative to wetter climates. WTF and CMB-based GRR estimates exhibited low agreement in arid and semi-arid zones, where most WTF-derived GRRs exceeded CMB values by over an order of magnitude. While this can be explained by differing dominance of focused vs diffusive recharge, we show influence from other factors including the inability of the WTF method to quantify low GRRs, impacts of land use change, and non-ideal conditions like river-aquifer connections. Major differences between the WTF and CMB methods are attributed to CMB reflecting pre-land clearing GRRs in many instances. This study serves as a comparative framework for evaluating the appropriateness and differences between the WTF and CMB methods which can be applied to groundwater recharge studies globally.