Abstract. An understanding of hydrological processes is vital for the sustainable management of groundwater resources, especially in areas where an aquifer interacts with surface water systems or where aquifer interconnectivity occurs. This is particularly important in areas that are subjected to frequent drought/flood cycles, such as the Cressbrook Creek catchment in Southeast Queensland, Australia. In order to understand the hydrological response to flooding and to identify inter-aquifer connectivity, multiple isotopes (δ²H, δ¹⁸O, ⁸⁷Sr/⁸⁶Sr, ³H and ¹⁴C) were used in this study in conjunction with a comprehensive hydrochemical assessment, based on data collected 6 months after severe flooding in 2011. The relatively depleted stable isotope signatures of the flood-generating rainfall (δ²H: −30.2 to −27.8‰, δ¹⁸O: −5.34 to −5.13‰ VSMOW) were evident in surface water samples (δ²H: −25.2 to −23.2‰, δ¹⁸O: −3.9 to −3.6‰ VSMOW), indicating that these extreme events were a major source of recharge to the dam in the catchment headwaters. Furthermore, stable isotopes confirmed that the flood generated significant recharge to the alluvium in the lower part of the catchment, particularly in areas where interactions between surface waters and groundwater were identified and where diffuse aquifer recharge is normally limited by a thick (approximately 10 m) and relatively impermeable unsaturated zone. However, in the upper parts of the catchment where recharge generally occurs more rapidly due to the dominance of coarse-grained sediments in the unsaturated zone, the stable isotope signature of groundwater resembles the longer-term average rainfall values (δ²H: −12.6, δ¹⁸O: −3.4‰ VSMOW), highlighting that recharge was sourced from smaller rainfall events that occurred subsequent to the flooding. Interactions between the bedrock aquifers and the alluvium were identified at several sites in the lower part of the catchment based on ⁸⁷Sr/⁸⁶Sr ratios; this was also supported by the hydrochemical assessment, which included the modelling of evaporation trends and saturation indices. The integrated approach used in this study facilitated the identification of hydrological processes over different spatial and temporal scales, and the method can be applied to other complex geological settings with variable climatic conditions.