1. Palaeolimnological analyses of fossil diatoms and pigments were conducted in four lakes of the Qu'Appelle Valley, Saskatchewan, Canada, to quantify the effect of upstream depositional basins on lake response to urban and agricultural human activities. Pasqua, Echo, Mission and Katepwa lakes exhibit similar modern limnological characteristics, lie sequentially downstream from urban point sources of growth-limiting nitrogen (N), yet drain similarly large areas of farmland (38–40 × 103 km2). 2. Analyses indicated that all lakes were naturally productive, contained eutrophic diatoms (i.e. Stephanodiscus niagarae, S. hantzchii, S. parvus and Aulacoseira granulata), and supported blooms of colonial (as myxoxanthophyll) and potentially toxic N-fixing cyanobacteria (aphanizophyll), even prior to the onset of European settlement (ca. 1890) and urban development (ca. 1930). 3. The onset of agricultural practices ca. 1890 had only modest effects on algal communities in the Qu'Appelle lakes, with subtle increases in eutrophic diatom species (Pasqua, Mission and Katepwa lakes) and 25–50% increases in pigment-inferred algal abundance (Echo, Mission and Katepwa lakes). 4. Despite naturally high production, total algal abundance (β-carotene) in upstream Pasqua Lake increased by more than 350% after intense urbanization beginning ca. 1930, while eutrophic diatoms became more common and cyanobacteria populations increased ten-fold. Principal components analysis (PCA) explained 64% of diatom variance, and identified three eras corresponding to baseline, pre-agricultural communities (1776–1890), an era of high production (ca. 1925–1960) and recent variable community composition following tertiary treatment of urban sewage (ca. 1977–1990). 5. Analyses of three downstream lakes demonstrated that urban impacts following 1930 remained evident in fossil profiles of β-carotene and myxoxanthophyll, but that large blooms of N-fixing cyanobacteria were restricted to the past 25 years at downstream Mission and Katepwa lakes. Similarly, PCA showed that fossil diatom assemblages exhibited little directional variation until the 1970s. 6. Together, these analyses support the hypothesis that upstream lakes were effective at reducing the impacts of point-source urban nutrients on downstream lakes. In contrast, diffuse agricultural activities had only limited impacts on water quality and these were less well ameliorated by upstream basins. [ABSTRACT FROM AUTHOR]