Lake Coeur d'Alene (CDA) and the floodplain along the CDA River, Idaho, USA contain metal-enriched sediments due to historical mining activities in the upstream world-class CDA mining district. The potential remobilization of metals from these sediments and their transport to the overlying water may affect water quality within the CDA River basin. Our objectives are to determine whether the sediments act as sources or sinks of metal contaminants, assess what processes control the metal flux, and predict how anthropogenic alteration of trophic status will influence the flux. Sediment and interstitial water from the lake and a nearby pond were collected to determine concentrations of As, Cd, Fe, Mn, Pb, and Zn. Measured interstitial water concentrations of As, Cd, and Pb in lake sediments exceed EPA's toxic limit and Zn concentrations exceed EPA's acute limit, whereas the floodplain pond interstitial water did not exhibit any elevated metal concentrations. Benthic fluxes in each system were calculated and compared. Modeling of organic matter diagenesis was performed to assess factors that affect the location of redox boundaries and their impact on the direction and magnitude of metal benthic fluxes. This information is used to predict how changes in the trophic status of the lake and pond might influence redox conditions, benthic fluxes of metals, and water quality in these systems.