Assemblages of dinoflagellate cysts in lakebed sediments across the deep, meromictic basin of Sluice Pond (Lynn, Massachusetts) were compared with measurements of water quality and sediment geochemistry and with testate amoeba and tintinnid assemblages. Lakebed sediments below oxygenated waters (DO >2 mg/L) contain diverse testate amoebae, but sparse Peridinium willei-dominated dinoflagellate cyst assemblages. Sediments collected under hypoxic conditions (DO < 2 mg/L) showed higher preservation of organic carbon and nitrogen, and these deep basin sediments are characterised by diverse dinoflagellate cyst assemblages, but sieved microfossil assemblages are typically dominated by the planktonic Codonella cratera and the pseudo-planktonic Cucurbitella tricuspis. Strong inverse relationships of cysts of Peridinium willei (R2 = 0.81) and Difflugia oblonga tests (R2 = 0.7) with water depth are attributed to variations in bottom water oxygen concentrations. Both ecological and taphonomic factors must be considered when reconstructing palaeoenvironments from microfossil assemblages.