It is widely agreed that the Earth’s atmosphere and oceans have undergone major redox changes over the last 2.5 billion years. However, the magnitude of these shifts remains a point of debate because it is difficult to reconstruct concentrations of dissolved O2 from indirect proxies in sedimentary archives. In this study, we show that an additional complicating factor that is rarely considered may be the pH of the water column. We analyzed rock samples from the early Jurassic Towaco Formation in the Newark basin (eastern USA), comprising deposits of a rift lake that became temporarily redox stratified. New biomarker evidence points to increasingly saline aquatic conditions during the second half of the lake’s history, with a salinity stratification that induced redox stratification, including evidence for water column anoxia, and that state may also explain the disappearance of macrofauna at this time. Distinctive lipid biomarker assemblages and stable nitrogen isotope data support previous mineralogical indications that the lake was alkaline (pH ≥ 9) during its saline episode. Despite the biomarker and macrofaunal evidence for anoxia, ratios of Fe/Al and FeHR/FeT show only small to no enrichments in the anoxic horizon compared to oxic facies in the same section – counter to what is commonly observed in anoxic marine settings. Molybdenum, As, V, U and to some degree Cd show enrichments in the anoxic interval, whereas Co, Ni, Cu, Zn and Cr do not. These patterns are most parsimoniously explained by differential pH effects on the solubility of these elements. Extrapolating from these observations in lacustrine strata, we speculate that a secular increase in seawater pH over Earth’s history as recently proposed may have helped modulate the magnitude of trace metal enrichments in marine shales, although other factors such as atmospheric and oceanic redox likely dominated the observed enrichment patterns. Further, a decrease in the solubility of ferrous iron, a major O2 sink, with increasing pH may have contributed to ocean oxygenation. In summary, our results highlight the potential importance of pH in influencing global biogeochemical cycles for multiple elements and for the interpretation of ancient nitrogen isotope signatures.