This study compares baseflow estimates using chemical mass balance, local minimum methods, and recursive digital filters in the upper reaches of the Barwon River, southeast Australia. During the early stages of high-discharge events, the chemical mass balance overestimates groundwater inflows, probably due to flushing of saline water from wetlands and marshes, soils, or the unsaturated zone. Overall, however, estimates of baseflow from the local minimum and recursive digital filters are higher than those based on chemical mass balance using Cl calculated from continuous electrical conductivity measurements. Between 2001 and 2011, the baseflow contribution to the upper Barwon River calculated using chemical mass balance is between 12 and 25% of the annual discharge with a net baseflow contribution of 16% of total discharge. Recursive digital filters predict higher baseflow contributions of 19 to 52% of discharge annually with a net baseflow contribution between 2001 and 2011 of 35% of total discharge. These estimates are similar to those from the local minimum method (16 to 45% of annual discharge and 26% of total discharge). These differences most probably reflect how the different techniques characterise baseflow. The local minimum and recursive digital filters probably aggregate much of the water from delayed sources as baseflow. However, as many delayed transient water stores (such as bank return flow, floodplain storage, or interflow) are likely to be geochemically similar to surface runoff, chemical mass balance calculations aggregate them with the surface runoff component. The difference between the estimates is greatest following periods of high discharge in winter, implying that these transient stores of water feed the river for several weeks to months at that time. Cl vs. discharge variations during individual flow events also demonstrate that inflows of high-salinity older water occurs on the rising limbs of hydrographs followed by inflows of low-salinity water from the transient stores as discharge falls. The joint use of complementary techniques allows a better understanding of the different components of water that contribute to river flow, which is important for the management and protection of water resources .