The Earth's redox evolution has been commonly assumed to have played a key role in shaping the evolutionary history of the biosphere. However, whether and how shifts in marine redox conditions are linked to key biotic events – foremost the rise of animals and the ecological expansion of eukaryotic algae in the late Proterozoic oceans – remains heavily debated. Our current picture of global marine redox evolution during this critical interval is incomplete. This is particularly the case for the Tonian Period (∼1.0 to ∼0.717 Ga), when animals may have diverged and when eukaryotic algae began their rise in ecological importance. Here, we present new uranium isotope (δ²³⁸U) measurements from Tonian carbonates to fill this outstanding gap. These Tonian carbonates (∼1000–800 Ma) record variable δ²³⁸U values, indicating temporal variation in global marine redox through this under-investigated time interval. Arguably the most interesting feature of this new δ²³⁸U dataset is an interval of anomalously negative δ²³⁸U values (<−1‰) that represent among the most negative stratigraphically continuous values reported to date. These low δ²³⁸U values are best explained by prevalent shallow-water anoxia, potentially driven by increases in productivity in a low-O₂ Tonian Earth system. We thus provide compelling evidence for extensive shallow marine anoxia just prior to or coincident with Neoproterozoic ecological shifts.