We employ water-isotope tracers and multi-proxy paleolimnological records to characterize contemporary controls on water balances of floodplain lakes in the Athabasca Delta, Canada, within the context of its hydroecological evolution over the 20th century. The insight gained from these approaches is necessary to gauge the hydroecological resiliency of the Athabasca Delta to past and future changes in Athabasca River flow regime. Results obtained from three lakes located in different regions of the Athabasca Delta indicate that hydroecological conditions were strongly affected by an engineered meander cut-off on the Athabasca River in 1972, intended to maintain flow in the river main stem, and a natural bifurcation of one of the major distributaries (Embarras River) in 1982, in response to progressive overextension of the delta to the east. Climate warming and naturally declining river discharge have also contributed to directional change. Recent drying trends reconstructed from sediment cores at two of the three lakes are likely representative of rapidly evolving hydroecological conditions in the south-eastern sector, based on mapping of a recent high-magnitude ice-jam flood that failed to recharge this portion of the delta, while wetting in the region of the third lake due to increased frequency of river flooding reflects increasing diversion of Athabasca River flow northward. Our findings highlight the hydroecological sensitivity of the Athabasca Delta to changes in the magnitude and timing of discharge in the Athabasca River and heighten the need for informed management strategies to safeguard the integrity of this unique wetland ecosystem.