The Drummond Nature Reserve (DNR), a high-value conservation area 100km northeast of Perth, Western Australia, contains two rare freshwater claypans and a diverse range of rare and threatened vascular plants. Groundwater/surface-water interactions were investigated via isotopic (δ18OandδD) and major ion analysis. The groundwater chemical and isotope analyses combined with nutrient data allowed for the assessment of potential hydro-logically derived threats to the claypans and their associated conservation values. Groundwater composition is typically Na–CltoNa–Mg–Cl; whereas the claypan’s ephemeral fresh surface water is Na–Cl–HCO3. Distinct δ18O and δDisotopic signatures for the claypan surface waters and adjoining groundwaters indicate that there currently is minimal connection between these two hydrological systems. Hence the current threat to the freshwater claypans and associated biota from rising saline and acidic groundwater is minimal. Elevated nutrient (N) levels identified in groundwaters along the reserve’s western boundary may be linked to fertiliser regimes employed in adjoining agricultural lands. The ecosystem associated with the southwest claypan is particularly vulnerable to N and P inputs via surface-water flows, which could cause algal blooms, vegetation degradation and weed infestation.