Paleoecological investigations of sediments deposited downstream of freshwater springs have the potential to reconstruct the environmental history of source aquifers and their catchments, thereby allowing for the study of long-term changes in these important hydrological systems. In an exploratory investigation, a 76-cm sediment column was obtained from a spring bed in Scarborough, southern Ontario, Canada. The column represents about 160 years of accumulated sediment. Siliceous microfossils, including diatoms, chrysophyte cysts, phytoliths and plates of testate amoebae (Rhizopoda), were identified and enumerated. Over the ~160-year period, siliceous remains track a gradual transition from a slow river environment in the early 1800s to a spring-fed pond environment by the late-1800s, hurricane-induced flooding, and the eventual slowing and drying of the spring in the latter half of the twentieth century. Basal, pre-settlement sediments contain a cosmopolitan assemblage of diatom taxa and testacean plates of the genus Lesquereusia. Between ~1880 and ~1954, fossils of aquatic species occur only in trace amounts, indicating increased deposition of clastic material and poor conditions for survival, but unbroken microfossils indicate that preservation of opaline remains was not a problem. Despite low concentrations of microfossils in this interval, chrysophyte and testacean survival was favoured over diatoms. In 1954, a thick layer of sediment was deposited by hurricane-induced flooding, confirmed by high phytolith concentrations from terrestrial sources. Since ~1960, epiphytic diatoms, reflecting dense macrophyte growth and higher productivity, dominate the diatom assemblage. Some of the recent diatom taxa are also salinity-tolerant, reflecting possible groundwater salinification. Chrysophyte cysts are relatively abundant at the top of the sediment column, but recent concentrations are lower than pre-settlement levels, likely reflecting an increased nutrient load. Recent increases in vegetation in and around the spring are also inferred by high concentrations of testacean plates and phytoliths. These paleoecological data match historical records and data from previous investigations of fossil aquatic insect larvae. These approaches show promise for relating changes in siliceous microfossils to human impacts and natural changes in spring habitats, their catchments and the quality of groundwater.