Abstract The land‐to‐ocean aquatic continuum (LOAC) carries contaminants, nutrients, and particulate carbon (C) from inland aquatic systems to the sea, which can impact regional biogeochemical budgets and local ecosystem health. Climate change and other anthropogenic influences (e.g., hydroelectricity) will affect the LOAC across varied watersheds. Qualifying the source and fate of particulate organic C across the LOAC can help evaluate regional biogeochemical interactions. Here, we measure isotopic, elemental, and molecular geochemical parameters of particulate matter from five components (lake, river and estuary suspended particulate matter, lake and estuary surface sediments) across the Romaine River watershed to fingerprint if the terrigenous, watershed signal is transported, lost or transformed on its way to the coast. We also measure total mercury (THg) to explore the relationship between organic matter source and mercury. Suspended particulates from river water and lake sediments in the watershed revealed the highest concentrations of organic C (OC), with the lowest concentrations sampled where the river meets the estuary. Lake sedimentary isotopic compositions ( δ 13 C org ) aligned closest to C3 plants and stored the highest lignin concentrations. Although there was molecular evidence of terrestrial export from the continental watershed, δ 13 C org values in coastal estuary sediments suggest marine microbial contributions dominated the low amounts of OC accumulating. There was a significant, positive relationship between the amount of OC and THg concentrations in watershed sediments. Geochemical measurements suggest preferential retention of terrestrial derived over microbially sourced OC, and that retention of this terrestrial material led to storage of THg within watershed components.