Eagle Harbor in Puget Sound, WA became a Superfund site in 1987 due to polycyclic aromatic hydrocarbons (PAHs) released chronically from a nearby creosoting facility. Early studies here (1983-86) demonstrated up to an ~80% prevalence of toxicopathic liver lesions, including neoplasms, in resident English sole (Parophrys vetulus). These lesions in English sole are consistently associated with PAH exposure in multiple field studies, and one laboratory study. Later studies (1986-88) incorporated biomarkers of PAH exposure and effect, including hepatic CYP1A expression and xenobiotic-DNA adducts, and biliary fluorescent aromatic compounds (FACs). Before site remediation, lesion prevalences and other biomarker values in this species from Eagle Harbor were among the highest compared to other sites in Puget Sound and the US Pacific Coast. To sequester PAH-contaminated sediments, in 1993-1994, a primary cap of clean sediment was placed over the most-contaminated 54 acres, with a 15-acre secondary cap added from 2000-2002. Lesion prevalences and biomarker values before primary capping were reduced compared to 1983-86, consistent with facility closure in 1988 and shore-based source controls begun in 1990. Liver lesion risk, hepatic CYP1A activities, and levels of biliary FACs from fish collected immediately after and at regular intervals up to 2 years after primary capping were variable relative to pre-capping. Over the entire monitoring period since primary capping (128 months), but particularly after 3 years, there was a significantly decreasing trend in biliary FACs, hepatic DNA adducts and lesion risk in English sole. In particular, lesion risk has been consistently low (< 0.20) compared to primary cap initiation (set at 1.0), from ~4 years after primary capping through April 2004. These results show that the sediment capping process has been effective in reducing PAH exposure and associated deleterious biological effects in a resident flatfish, and that longer term monitoring of pollutant responses in biological resources, such as resident fish, is needed in order to demonstrate the efficacy of this type of remediation.