Over 50 years ago, a marine estuary was converted to a wastewater stabilization basin for treatment of primarily pulp and paper effluent. As a result, the basin was immediately converted to a “freshwater” environment and subsequently accumulated a thin layer of black, organic-rich sediment containing varying amounts of dioxins and furans, metals, polycyclic aromatic hydrocarbons and petroleum hydrocarbons. Previous studies on the site have shown that the majority of this contamination in the basin appears to have been contained within this black sediment layer and not migrated to any significant extent into the original underlying marine sediments. The purpose of this study is to examine sediment porewater chemistry changes that have occurred over 51 years of operation of the stabilization basin with the intent of better understanding why contamination has been minimal into the underlying natural marine sediments. Field and laboratory testing is presented to characterize the physical, chemical and mineralogical sediments in the basin. Porewater chemistry profiles obtained from this work are then used in combination with a one-dimensional contaminant transport model to examine the role of diffusion, sorption and upward groundwater flux in the porewater profiles found for the sediments.