Microfossil studies from Sluice Pond, Massachusetts, identified two environmental perturbations that impacted algal and protozoan communities: (1) natural eutrophication and water column mixing driven by the mid-Holocene drought and (2) cultural eutrophication, increasing bottom water anoxia, and toxicity accompanying human settlement. SP09 KC2 from the deep basin of this partially meromictic pond has an abundant and diverse record of dinoflagellate cysts spanning 11,400 years. Bottom water anoxia appears to have prevented benthic protozoans from colonizing until lake levels fell throughout New England during the mid-Holocene drought. Lower lake levels allowed mixing of the water column and a thecamoebian fauna rich in centropyxids, Pontigulasia compressa, and Difflugia oblonga to flourish in SP09 KC2. This lowstand is marked by an unconformity spanning the mid-Holocene hemlock minimum (5400–3500 cal. BP) in SP07 PC4 and by an increase in nutrients in the water column allowing mesotrophic–eutrophic dinoflagellate taxa ( Peridinium cf. gatunense and Peridinium willei) to increase at the expense of Peridinium wisconsinense. Rising lake levels in response to the warm, wet climate are recorded by increasing abundances of protozoa tolerant of lower dissolved oxygen (DO) throughout Sluice Pond ~2200 cal. BP – the thecamoebians Arcella vulgaris, Difflugia protaeiformis, and Cucurbitella tricuspis and the ciliate Codonella cratera. Subsequent decline in lake level associated with late Holocene aridity allowed a diverse thecamoebian community to thrive until around 300 years ago when a more intense phase of eutrophication resulted from human impact. Bottom water anoxia due to enhanced biochemical oxygen demand (BOD) is recorded by the dominance of C. tricuspis in sediments rich in ragweed pollen and other weedy plants. Peak cyst concentrations in this interval in SP07 PC4 reflect cultural eutrophication leading to high primary productivity and low DO, promoting cyst preservation. Low microfossil concentrations in the surface sediments are attributed to low DO and toxicity.