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.