The later stages of Earth's transition to a permanently oxygenated atmosphere during the Great Oxidation Event (GOE; ∼2.43–2.06 Ga) is commonly linked with the suggestion of an “oxygen overshoot” during the ∼2.22–2.06 Ga Lomagundi Event (LE), which represents Earth's most pronounced and longest-lived positive carbon isotope excursion. However, the magnitude and extent of atmosphere-ocean oxygenation and implications for the biosphere during this critical period in Earth's history remain poorly constrained. Here, we present nitrogen (N), selenium (Se), and carbon (C) isotope data, as well as bio-essential element concentrations, for Paleoproterozoic marine shales deposited during the LE. The data provide evidence for a highly productive and well-oxygenated photic zone, with both inner and outer-shelf marine environments characterized by nitrate- and Se oxyanion-replete conditions. However, the redoxcline subsequently encroached back onto the inner shelf during global-scale deoxygenation of the atmosphere-ocean system at the end of the LE, leading to locally enhanced water column denitrification and quantitative reduction of selenium oxyanions. We propose that nitrate-replete conditions associated with fully oxygenated continental shelf settings were a common feature during the LE, but nitrification was not sufficiently widespread for the aerobic nitrogen cycle to impact the isotopic composition of the global ocean N inventory. Placed in the context of Earth's broader oxygenation history, our findings indicate that O2 levels in the atmosphere-ocean system were likely much lower than modern concentrations. Early Paleoproterozoic biogeochemical cycles were thus far less advanced than after Neoproterozoic oxygenation.