AbstractLate Devonian marine systems were characterized by major environmental perturbations and associated biotic community changes linked to climate change and widespread oceanic anoxia. Here, we provide high-resolution lipid biomarker chemostratigraphic records from the Upper Devonian Chattanooga Shale (Tennessee, USA) to investigate algal-microbial community changes in the southern Illinois Basin that were related to contemporaneous shifts in marine redox (as proxied by trace metals, Fe-species, and Corg/P) and salinity conditions (as proxied by B/Ga, Sr/Ba, and S/total organic carbon). The Frasnian was characterized by dominantly bacterial lipids (high hopane/sterane), near-marine salinity, and a shift from oxic to increasingly reducing conditions in response to increasing organic carbon sinking fluxes. Aryl isoprenoids and aryl isoprenoid ratios reveal that the O2-H2S chemocline was unstable and intermittently shallow (i.e., within the photic zone). The Frasnian-Famennian boundary was marked by a shift in microalgal community composition toward green algal (e.g., prasinophyte) dominance (lower C27 and higher C28 and C29 steranes), a sharp reduction in watermass salinity, and a stable O2-H2S chemocline below the photic zone, conditions that persisted until nearly the end of the Famennian. We infer that changing watermass conditions, especially a sharp reduction in salinity to possibly low-brackish conditions (<10 psu), were the primary cause of concurrent changes in the microalgal community, reflecting tolerance of low-salinity conditions by green algae. Transient spikes in moretane/hopane (M/H) ratios may record enhanced terrestrial weathering at the Frasnian-Famennian and Devonian–Carboniferous boundaries, triggered by coeval glacio-eustatic falls and increased inputs of soil organic matter. High M/H and pristane/phytane, in combination with low chemical index of alteration and K/Al, record a decrease in chemical weathering intensity during the Famennian that may have been due to contemporaneous climatic cooling, and a concurrent reduction in silt content may reflect stabilization of land surfaces by vascular plants and resulting reduced sediment yields. This study demonstrates the effectiveness of combining organic and inorganic geochemical proxies (including novel paleosalinity indices) for determination of environmental controls on the composition and productivity of plankton communities in paleomarine systems.