ABSTRACT The global increase in the frequency and intensity of cyanobacteria blooms has been widely attributed to changes in land‐use practices and climate variability, yet little is known of how toxicity has varied historically relative to cyanobacteria abundance. Fossil pigments from cyanobacteria and algae were quantified from shallow lake sediment core records using high‐performance liquid chromatography, whilst past concentrations of microcystin congeners were measured using liquid chromatography high‐resolution mass spectrometry. These metrics were combined with measures of sedimentary geochemistry (δ13C, δ15N, %N, %C, C:N ratio) to estimate how lake production and abundance of toxigenic cyanobacteria varied during the past ~300 years in two small lakes in New Brunswick, Canada. Harvey Lake is an impacted site with a history of intensive catchment land use, whilst Wheaton Lake is a relatively undisturbed reference site. Stratigraphically constrained cluster analysis (CONISS) revealed that primary production increased steadily in both lakes since the second half of the 20th century, whilst microcystin production increased by an order of magnitude after ca. 2000 CE. Fossil pigment concentrations were initially lower in Harvey Lake but shifted to more productive conditions after initial forest clearance and settlement and again after agricultural intensification during the 20th century. Although Wheaton Lake exhibited higher overall fossil pigment concentrations, including a pre‐colonial eutrophic interval (ca. 1680–1750 CE), this reference basin also underwent enrichment since ca. 1980, possibly reflecting longer growing seasons in the last 50 years. Although cyanobacterial pigments and microcystin concentrations were elevated in sediments deposited since ca. 2000 CE in both lakes, these variables were uncorrelated over the entire 300‐year record, with the pre‐colonial eutrophic interval in Wheaton Lake having low toxin concentrations. This pattern suggests either that cyanobacterial dominance and toxicity are regulated by different factors or that the preservation of microcystins and pigments is under unique controls. Statistical analyses showed that these small shallow maritime lakes are sensitive to relatively small land‐use perturbations within their catchments and that even undisturbed basins may be vulnerable to toxic cyanobacteria blooms in a warming climate.