A $200 million-dollar ecological restoration was initiated in 2013 to remediate the influence of heavy metal contamination of floodplain sediments along the Upper Clark Fork River (UCFR), Montana, USA. UCFR restoration activities included removing metal-laden floodplain sediments, lowering the floodplain to hydraulically reconnect to the river channel, and replanting floodplain vegetation along the river length being restored. The goal of these activities was to restore the structure and function of the floodplain ecosystem closer to which existed before the 1908 flood that transported contaminated sediment into the floodplain. We have monitored water quality, organic carbon chemistry, and metal dynamics across 13 sites within the UCFR corridor from 2017 to 2022 to assess the trajectory of the ecosystem in response to the restoration efforts. Organic carbon composition was measured qualitatively (by absorbance spectroscopy and fluorescence spectroscopy) and quantitatively (dissolved organic carbon [DOC] concentrations). We analyzed these data along with spatiotemporal flow patterns, nutrient concentrations, and aqueous metal concentrations measured by inductively coupled plasma mass spectrometry (ICP MS). Aromatic DOC composition was greater in the headwaters, and river flow is proportionally more influenced by inflow from mountain headwaters. Despite strong variation in aquatic ecosystem, microbial and algal activity across seasons, there was little evidence of seasonal variation in the DOC fluorescence characteristics from a given site. Arsenic, cobalt, and manganese concentrations decreased downstream, following the EPA expectations with restoration efforts. However, concentrations of aluminum, cadmium, chromium, copper, iron, nickel, lead, selenium, vanadium, and zinc were highly variable downstream, likely influenced by tributaries. Lastly, we observed filtration effects in metal concentrations (whole and filtered waters) where chelation to DOC, size partitioning, and transport of metals by particles likely contribute to variation of upstream and downstream. Understanding the drivers of metal variation and DOC character in the UCFR alongside other biogeochemical data offers insights into emerging signals of restoration efforts after severe metal contamination.