We used stable isotopes (δ18O and δ2H) and water chemistry to characterize the water balance and hydrolimnological relationships of 57 shallow aquatic basins in the Peace-Athabasca Delta (PAD), northern Alberta, Canada, based on sampling at the end of the 2000 thaw season. Evaporation-to-inflow ratios (E/I) were estimated using an isotope mass-balance model tailored to accommodate basin-specific input water compositions, which provided an effective, first-order, quantitative framework for identifying water balances and associated limnological characteristics spanning three main, previously identified drainage types. Open-drainage basins (E/I < 0·4; n = 5), characterized by low alkalinity, low concentrations of nitrogen, dissolved organic carbon (DOC) and ions, and high minerogenic turbidity, include large, shallow basins that dominate the interior of the PAD and experience frequent or continuous river channel connection. Closed-drainage basins (E/I ≥ 1·0; n = 16), in contrast, possess high alkalinity and high concentrations of nitrogen, DOC, and ions, and low minerogenic turbidity, and are located primarily in the relict and infrequently flooded landscape of the northern Peace sector of the delta. Several basins fall into the restricted-drainage category (0·4 # E/I < 1·0; n = 26) with intermediate water chemistries and are predominant in the southern Athabasca sector, which is subject to active fluviodeltaic processes, including intermittent flooding from riverbank overflow. Integration of isotopic and limnological data also revealed evidence for a new fourth drainage type, mainly located near the large open-drainage lakes that occupy the central portion of the delta but within the Athabasca sector (n = 10). These basins were very shallow (<50 cm deep) at the time of sampling and isotopically depleted, corresponding to E/I characteristic of restricted- and open-drainage conditions. However, they are limnologically similar to closed-drainage basins except for higher conductivity and higher concentrations of Ca2+ and Na+, and lower concentrations of SiO2 and chlorophyll c. These distinct features are due to the overriding influence of recent summer rainfall on the basin water balance and chemistry. The close relationships evident between water balances and limnological conditions suggest that past and future changes in hydrology are likely to be coupled with marked alterations in water chemistry and, hence, the ecology of aquatic environments in the PAD. Copyright © 2006 John Wiley & Sons, Ltd.