Repeated measurements over 3 years (2003–2005) were made on a series of lakes along a hydrological gradient in the Peace-Athabasca Delta (PAD), Canada, to characterize the role of river flooding on limnological conditions of northern floodplain lakes and to identify the patterns and timescales of limnological change after flooding. River floodwaters elevate concentrations of suspended sediment, total phosphorus (TP), SO4 and dissolved silica (DSi) and reduce concentrations of total Kjeldahl nitrogen (TKN), dissolved organic carbon (DOC) and most ions, which leads to increased limnological homogeneity among lakes. After flooding, limnological changes occur at two distinct timescales. In the weeks to months after flooding, water clarity increases as suspended sediments and TP settle out of the water column, but concentrations of DOC, SO4, TKN and ions do not change appreciably. However, in the absence of flooding for many years to decades, evaporative concentration leads to an increase in most nutrients, DOC and ions. Contrary to a prevailing paradigm, these results suggest that regular flooding is not required to maintain high nutrient concentrations. In light of anticipated declines in river discharge, we predict that limnological conditions in the southern Athabasca sector will become increasingly less dominated by the short-term effects of flooding, and resemble nutrient- and solute-rich lakes in the northern Peace sector that are infrequently flooded. Copyright © 2011 John Wiley & Sons, Ltd.