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Evaluation of large lake response to centennial changes in land use and climate can be complicated by high spatial and hydrological complexity within their catchments, particularly in regions of low relief. Furthermore, large lakes can exhibit abrupt changes in structure and function that obscure causes of eutrophication.We provide the first quantification of historical trends in lake production, cyanobacterial abundance, sediment geochemistry and diatom composition since c. 1800 in Lake Manitoba, the 29th largest lake in the world, and compared them to Lake Winnipeg, a morphologically similar, adjacent basin with a 10‐fold larger catchment and an abrupt increase in production around 1990.Before 1900, Lake Manitoba was mesotrophic, with low sedimentary concentrations of carbon, phosphorus, nitrogen, cyanobacteria and algal pigments, as well as assemblages of low‐light‐adapted benthic diatoms. Analysis of pigment time‐series with hierarchical generalised additive models revealed that Lake Manitoba eutrophied during 1900–1930 as a consequence of the development of intensive agriculture within its local catchment, but thereafter exhibited stable cyanobacterial densities with limited expansion of N2‐fixing cyanobacteria despite persistent eutrophication.Lake Manitoba did not undergo an abrupt change as seen in Lake Winnipeg.These findings suggest that catchment size had little influence on water quality degradation and that nutrient influx from proximal agricultural sources was sufficient to initially degrade these large prairie lakes. The abrupt change in Lake Winnipeg around 1990 required additional intensification of local land use that did not occur in the Lake Manitoba catchment. [ABSTRACT FROM AUTHOR]

1. Lake managers suspect that taste and odour-causing algal blooms are increasing in frequency and intensity, although long-term monitoring records are scarce, and a number of critical scientific and management questions remain unanswered. 2. In nutrient-poor lakes and reservoirs, these events are caused primarily by sporadic outbreaks of some chrysophyte algae, which leave identifiable markers in lake sediments. We examine the siliceous remains of these organisms in more than fifty boreal lakes at broad temporal and spatial scales. 3. Colonial scaled chrysophytes, including the taste and odour-causing Synura petersenii, have increased markedly in more that 90% of the lakes examined since pre-industrial times. 4. Detailed stratigraphic analyses of two lakes show a rise in the abundance of colonial taxa in the 1930s to 1950s, with a sharp increase over the past two decades. 5. An examination of biogenic silica and biological ratios in Crosson Lake, Ontario, Canada, indicate that these changes represent true increases in the absolute abundance of colonial chrysophytes. 6. Rapid increases over the past two decades indicate that these trends are the result of one or more anthropogenic stressors that are operating at a broad, regional scale. [ABSTRACT FROM AUTHOR]