Phytoplankton assemblages in shallow marine environments are being impacted by anthropogenic climate change, but long-term outcomes of these changes are uncertain. Investigation of past neritic calcareous nannoplankton can help us understand the fate these ecosystems face. In this study, a Canonical Correspondence Analysis (CCA) of calcareous nannofossils and X-ray fluorescence geochemistry was used to determine how past planktonic ecosystems were influenced by paleoenvironmental parameters on the eastern side of the Late Cretaceous Western Interior Seaway in the Cenomanian (ca. 95–93 Ma). Samples were collected every 10 cm from the Graneros Shale Greenhorn Formation at an outcrop in northwestern Iowa to determine high resolution changes in assemblages and paleoenvironments. Nannofossil diversity outside of a few small intervals ranges is high (generally 30–60 species) with abundant small Biscutum constans, confirming other publications that show elevated diversity in Cretaceous nearshore settings. The CCA results imply assemblages were most influenced by terrigenous influence, wet vs. dry climate, and changes in water mass source. Cretaceous nannofossil paleoecology was also revised based on the CCA results. Size differentiation of nannofossil taxa may highlight more complexity in environmental preferences that have been largely overlooked. After the initial transgression of the Greenhorn Sea into the region, the climate became wetter and terrigenous influence in the area was high. The peak of terrigenous influence corresponds with elevated nannofossil diversity but a lack of microfauna, which may indicate a similar oceanographic setting to the modern Gulf of Mexico nearshore dead zone. As sea level continued to rise above this point, nannoplankton assemblages indicate a potential shift to a higher productivity, stratified water column. As the muddy Graneros Shale transitioned to a further offshore chalky Greenhorn Formation, a normal marine, cosmopolitan nannofloral assemblage became established. Nannofossil and geochemical evidence indicates high productivity from upwelling might be related to the change of deposition to chalk in the Greenhorn Formation. While only a single outcrop was investigated, the novel use of an integrated micropaleontological and geochemical analysis has shed light on the dynamics of how phytoplankton ecosystems were established and modified in shallow marine environments of the Cretaceous and could have important implications on modern shallow marine settings. Display omitted •Cenomanian nannofossils and geochemistry from the northwestern Iowa were investigated.•Multivariate statistical analysis revised nannofossil paleoecology.•Terrigenous influence, climate, and water mass controlled assemblages.•Evidence suggests development of a nearshore dead zone like environment.•Diversity was high, and communities were divided by depth and sediment tolerance.