Cores dating back to deglaciation were taken from three lakes in Atlantic Canada and analyzed for arcellaceans and pollen. Paleotemperatures and paleo-precipitation were calculated from the pollen data using transfer functions. A sudden warming is recorded by the pollen around 10,000 years B.P., followed by a general warming to the mid Holocene Hypsithermal, then by a decrease in temperature and increase in effective precipitation to the present. The three lakes, two in western Newfoundland and one in eastern Nova Scotia, contain similar late glacial (13-10 ka), early Holocene (10-8 ka), mid Holocene (8-4 ka), and late Holocene (4-0 ka) arcellacean assemblages. Immediately following retreat of the ice sheets, Centropyxis aculeata, Centropyxis constricta, Difflugia oblonga, Difflugia urceolata, and Difflugia corona were common. The latter part of the late glacial is characterized by sparse assemblages dominated by C. aculeata. The arcellacean record thus suggests a climatic reversal in Atlantic Canada between 11,500 and 10,000 years B.P., analogous to the Younger Dryas, although this is not recorded by the pollen. Species diversity increased sharply at the beginning of the Holocene, and D. oblonga is the dominant taxon in early Holocene sediments. Difflugia oblonga remained common through the mid Holocene, but percentages of C. aculeata were very low, and Pontigulasia compressa and Difflugia bacillifera peaked in abundance during the Hypsithermal. The late Holocene is characterized by a resurgence in C. aculeata at the expense of other taxa. The increase in Heleopera sphagni and Nebella collaris since 5,000 years B.P. at the two sites in southwestern Newfoundland reflects paludification in response to increased precipitation since the Hypsithermal. Because the changes in arcellacean assemblages are regionally synchronous in all three lakes and coincide with climatically driven vegetational successions indicated by the pollen record, arcellaceans appear to respond to climatic change, and thus may be useful paleoecological and paleolimnological indicators. With their quicker generation time, these protists may be better suited than pollen to recording short-lived phenomena, like the mid-Holocene Hypsithermal and the Younger Dryas reversal.