When acidic groundwater flows into an aquatic system the sediment water interface (SWI) acts as a transition zone between the groundwater and lake water, and often exhibits strong physical and biogeochemical gradients. The fate of groundwater-borne solutes, such as Fe(II), is determined by the balance between the exposure time during transport across the SWI and the reaction time within the SWI, however the relative role of groundwater seepage rates and iron kinetics on acidity generation in lakes is unknown. Porewater seepage velocities, porewater chemical profiles, and limnological data were collected across multiple field campaigns over the last two decades, in acid Mine Lake 77, in Lusatia, Germany. This rare data set was analyzed using a Damköhler approach that compares exposure and reactions timescales, to determine that Fe(II) would typically be transported with little reaction across the SWI, spatially separating it from sediment-processes that produce alkalinity and providing a source of acidity to the lake. This Damköhler analysis further showed that remediation should be focused on reducing groundwater seepage velocities and enhancing exposure times. Strategic planting of submerged benthic macroalgae would slow groundwater inflows, as well as oxygenating overlying waters and supplying organic matter to the sediments. A similar Damköhler analysis could be used to assess the fate of any groundwater-borne reactive chemicals (e.g. phosphorus) into lakes and streams.