The 1.1 Ga Midcontinent Rift (MCR) is a thick volcanic-sedimentary succession that forms a curvilinear belt through central North America and crops out along its northern apex around Lake Superior. Sedimentary units of the MCR have been long interpreted as fluvial-lacustrine and invited a number of studies on the early evolution of life in non-marine habitats. One of the key units is the siliciclastic Nonesuch Formation, thought to record deposition in a large lake. However, recent sedimentological observations indicate the presence of marine incursions. To further test this interpretation, we analysed trace element abundances in a broad suite of samples from multiple drill cores through the Nonesuch Formation. We aimed to differentiate geochemical influences of sediment provenance from post-depositional hydrothermal overprint and thereby identify authigenic enrichments in fluid-mobile elements that are indicators of primary environmental conditions. Our results reveal discrete enrichments in Mo and U in organic- and sulphide-rich horizons, which are most parsimoniously interpreted as marine signatures. This conclusion is supported by Sr/Ba ratios, which suggest mixing between freshwater and saltwater, and by rare cm-thick gypsum in the upper Copper Harbor Formation immediately below the Nonesuch rocks. The gypsum displays δ34S values of +25.9 ± 0.6‰, consistent with input of marine sulphate at least during parts of the basin's history. Collectively, our geochemical data support the sedimentological interpretation that this portion of the MCR archives a marine-influenced estuarine system. Although this conclusion rules out that microbial life documented from the MCR was living in exclusively freshwater habitats, the Nonesuch Fm and associated rocks still hold important clues about organisms that were capable of withstanding salinity gradients and bridging the gap between the marine and non-marine environments of the mid-Proterozoic.