Human activities and climate change have greatly altered flooding regimes in many of the world's river deltas, but the impact of such changes remains poorly quantified on decadal to multidecadal timescales. This study identified the response of delta lake primary production (measured as the concentration of sedimentary pigments) to variations in flood frequency using spatial surveys and paleolimnological analyses of lakes in the Peace-Athabasca Delta (PAD), Canada. Surveys of 61 lakes spanning a range of hydrological conditions showed that those lakes that received flood waters less frequently were associated with elevated algal production (surface sedimentary pigments) and, in some lakes, increased growth of emergent macrophytes and epiphytic diatoms. Paleolimnological analyses of five lakes corroborated the contemporary spatial survey results by showing that production of pigments from most algal groups increased during recent periods of lower flood frequency in the 20th century as determined from increases in cellulose-inferred lake-water oxygen isotope composition and plant macrofossils, but remained stable in a ‘reference’ basin. In general, past periods of elevated algal production coincided with the increased abundance of submerged macrophytes or emergent vegetation that provide habitat for attached algae. These results suggest that interdecadal declines in river discharge arising from increased aridity, hydrologic regulation or consumptive water use will cause long-term increases in primary production and alter ecosystem processes (carbon sequestration, biological diversity) in aquatic delta ecosystems similar to the PAD where lakes become nutrient-rich in the absence of flooding.