This study demonstrates the importance of the conceptual hydrogeological model for the estimation of groundwater recharge rates in an alluvial system interconnected with an ephemeral or intermittent stream in south-east Queensland, Australia. The losing/gaining condition of these streams is typically subject to temporal and spatial variability, and knowledge of these hydrological processes is critical for the interpretation of recharge estimates. Recharge rate estimates of 76–182 mm/year were determined using the water budget method. The water budget method provides useful broad approximations of recharge and discharge fluxes. The chloride mass balance (CMB) method and the tritium method were used on 17 and 13 sites respectively, yielding recharge rates of 1–43 mm/year (CMB) and 4–553 mm/year (tritium method). However, the conceptual hydrogeological model confirms that the results from the CMB method at some sites are not applicable in this setting because of overland flow and channel leakage. The tritium method was appropriate here and could be applied to other alluvial systems, provided that channel leakage and diffuse infiltration of rainfall can be accurately estimated. The water-table fluctuation (WTF) method was also applied to data from 16 bores; recharge estimates ranged from 0 to 721 mm/year. The WTF method was not suitable where bank storage processes occurred.

High and variable levels of salinity were investigated in an intermittent stream in a high-rainfall area (∼800 mm/year) of the Mt. Lofty Ranges of South Australia. The groundwater system was found to have a local, upslope saline lens, referred to here as a groundwater salinity ‘hotspot’. Environmental tracer analyses (δ¹⁸O, δ²H, ⁸⁷/⁸⁶Sr, and major elements) of water from the intermittent stream, a nearby permanent stream, shallow and deep groundwater, and soil-water/runoff demonstrate seasonal groundwater input of very saline composition into the intermittent stream. This input results in large salinity increases of the stream water because the winter wet-season stream flow decreases during spring in this Mediterranean climate. Furthermore, strontium and water isotope analyses demonstrate: (1) the upslope-saline-groundwater zone (hotspot) mixes with the dominant groundwater system, (2) the intermittent-stream water is a mixture of soil-water/runoff and the upslope saline groundwater, and (3) the upslope-saline-groundwater zone results from the flushing of unsaturated-zone salts from the thick clayey regolith and soil which overlie the metamorphosed shale bedrock. The preferred theory on the origin of the upslope-saline-groundwater hotspot is land clearing of native deep-rooted woodland, followed by flushing of accumulated salts from the unsaturated zone due to increased recharge. This cause of elevated groundwater and surface-water salinity, if correct, could be widespread in Mt. Lofty Ranges areas, as well as other climatically and geologically similar areas with comparable hydrogeologic conditions.