Investigation of the occurrence, distribution and bioavailability of PFCs in the lower Apalachicola River and estuary was accomplished utilizing the passive in-situ polar organic integrative sampler (POCIS) in concert with historical (1986-1987 through 2006-2007) biota and sediment samples from NOAA's Mussel Watch program. PFCs were detected in archived oyster and sediment samples and in the water column via passive sampling. Concentrations ranged from < LOD to 4.7ng/g wet weight, oysters; <LOD to 2.5ng/g, wet weight sediment; and 0.3-59ng/L, water. PFCs concentrations were not statistically different (p > 0.05) in oyster and sediment samples among sampling sites. Temporally, there was a significant increase in PFCs concentrations in oysters from 1986-1987 through 2002-2003; however concentrations dramatically decrease for the remaining sampling years. No significant temporal trend was observed for the sediment samples. Spatially, PFCs water concentrations were significantly different (p < 0.01) with upriver samples having higher concentrations than samples from the bay. The results of this study provide a baseline assessment of the lower Apalachicola River and estuary and may allow prediction of potential impacts in this ecosystem.