Globally, Upper Devonian sedimentary successions are characterized by multiple organic-rich strata associated with dysoxic to anoxic conditions and biological turnover of varying magnitude, including the Lower and Upper Kellwasser intervals. The cause or causes of the Kellwasser extinction and their relationship to coeval environmental conditions remains actively debated. Here we show that organic-walled microfossils (OWMs) are preserved within the Kellwasser intervals at two localities in western New York State that are otherwise devoid of macrofossils. While OWMs are significantly more abundant within the Upper Kellwasser interval, the assemblages are slightly more diverse within the Lower Kellwasser interval, including two distinct smooth-walled leiosphere populations based on size and, in the more proximal locality, acanthomorphic (spinose) forms. Mo and U concentrations at these localities range from 1–86 ppm and 2–14 ppm respectively, and support oxygen stress, but not persistent anoxia or euxinia, through these events. Notably the Lower Kellwasser exhibits both greater OWM variability and more evidence of anoxic conditions, while the Upper Kellwasser exhibits relatively consistent OWM assemblages and more dysoxic conditions. We interpret OWM abundance, especially large leiosphere forms, as a possible signal of algal blooms potentially associated with eutrophication. Our results suggest that eutrophication may have played a larger role during the Lower Kellwasser event than during the Upper Kellwasser event and demonstrate how OWMs can provide an important link between primary productivity, eutrophication, and the deposition of organic rich-strata.