Acetolysis, an oxidising technique common in palynological preparation, is beneficial for pollen analysts who employ it to remove ‘unwanted’ organic matter from peat and lake samples. Since this technique was introduced by G. Erdtman in 1934, however, several researches have noted concerns, such as the destruction of thin-walled pollen grains in addition to non-sporopollenin pollen components, and selective destruction of protoperidinioid dinoflagellate cysts. Desmids are conjugate green algae with a wide range of environmental preferences whose half-cells are known from sediments dating back to at least the Neogene (possibly as far back as the Devonian), and they have proven useful in modern and palaeolimnological studies (e.g. as indicators of nutrient loading, anthropogenic impact and drought). Desmids are rarely mentioned in palynological studies, however, except to illustrate fluvial transport to nearshore marine settings. A diverse desmid flora was found in samples processed without acetolysis from Smith's Bay in Lake Simcoe, and desmid and thecamoebian (testate amoeba) assemblage changes record eutrophication up-core. Very low concentrations of both desmids and Pediastrum, another group of algal non-pollen palynomorphs (NPP), record siltation and inhibition of photosynthesis attributed to two phases of land-clearing and agriculture (Wendat/Huron and Euro-Canadian). After acetolysis, the desmid abundance in the same residues drops significantly (between 36 and 100%, mean = 87%) and the assemblage is skewed towards the most robust Cosmarium spp. However, other low-relief NPP, like Pediastrum, may be easier to observe after acetolysis as they are not obscured by amorphous organic matter. Because of the observed detrimental impact acetolysis has on the desmid assemblage, recommendations include: (i) not acetolysing, as pollen and Pediastrum can be observed either way, or (ii) using a two-pronged approach where susceptible microfossils are observed pre-acetolysis and resistant ones observed post-acetolysis.