Algal palynomorphs can provide key ecological information about aquatic environments, yet the preservation potential for most varieties of algae is poorly understood. Cores from Pine Forest and Bray Area lakes, two manmade lakes in the Rolla area of south—central Missouri, USA, provided an opportunity to relate the algal palynomorphs in the top 9 cm of sediments to the processes that lead to preservation. By comparing algal palynomorphs in the sediments to the algal crop in the water, this study seeks to assess the effects of taphonomy on the assemblage in a palynological sample. The lakes were ecologically monitored four times in one year (late fall, spring, summer, winter) to determine the algal crop, and surficial sediment was sampled in Pine Forest Lake once in early winter. The annual average abundance of algae in the lake water was compared with sediment data, and statistical techniques (Kruskal—Wallis test, Mann—Whitney U-test and Pielou's Equitability index) were used to determine ecological stability in the sediments. While Sphaerocystis and Ceratium hirundinella did not apparently preserve well, moderate to high preservation potential was determined for Staurastrum and Botryococcus. In addition, Pediastrum simplex var. pseudoglabrum, P. integrum and P. boryanum var. pseudoglabrum were well preserved in the sediments. This preliminary study shows that a highly abundant algal species in the water may not be well preserved in the sediment. Therefore, higher resolution studies are needed to further explore the preservation potential of algae in lake sediments.