The Thirlmere Lakes National Park is located about 75 km west-south-west of Sydney in New South Wales, Australia. The Park contains five small freshwater lakes in a cut-off meander of a Tertiary-age river valley. Water levels in Thirlmere Lakes are known to have fluctuated over time, but little is known about their hydrogeology and hydrology. Over the last decade a strong decline in water levels has occurred, leading to concern in the local community. Since the cause of the decline is unknown, our project aims to identify the controlling factors for the lake water levels by investigating the spatio-temporal groundwater-surface water interactions and the degree of connectivity between the lakes. While the lakes contained sufficient surface water, we were able to measure lake water and groundwater temperature time series for the application of heat tracing techniques. A piezometric monitoring network has now been established to provide detailed information of the groundwater water levels near and between the lakes. The piezometer installation also allowed for a stratigraphic mapping of the shallow unconsolidated aquifer/aquitard systems. These stratigraphic logs show heterogeneities in the sedimentary sequence to an extent that, for individual lakes, different degrees of connectivity and mechanisms of groundwater-surface water interaction can be anticipated. Results from the heat tracing analysis illustrate that locations with a low thermal conductivity, which is typical for the prevalent peat layers, show low or stagnant groundwater-surface water exchange; whereas the locations with higher thermal conductivity have higher and gaining groundwater flows. Even during the recent drying phase, some lakes appear to have a net groundwater gain, which is an indication that the declining lake levels are dominated by evaporation. Predominantly losing conditions are expected if the lakes were drying primarily as a result of declining groundwater levels. Hence, in response to recent declining surface water levels, the gaining portions of the lakes might be receiving groundwater inflow from connected shallow conductive layers. Without these groundwater contributions the lakes would likely dry much faster.