The goal of this article is to summarize new biological monitoring information on perfluorinated compounds (PFCs) in aquatic ecosystems (post-2005) as a followup to our critical review published in 2006. A wider range of geographical locations (e.g., South America, Russia, Antarctica) and habitats (e.g., high-mountain lakes, deep-ocean, and offshore waters) have been investigated in recent years enabling a better understanding of the global distribution of PFCs in aquatic organisms. High concentrations of PFCs continue to be detected in invertebrates, fish, reptiles, and marine mammals worldwide. Perfluorooctane sulfonate (PFOS) is still the predominant PFC detected (mean concentrations up to 1900 ng/g ww) in addition to important concentrations of long-chain perfluoroalkyl carboxylates (PFCAs; sum PFCAs up to 400 ng/g ww). More studies have evaluated the bioaccumulation and biomagnification of these compounds in both freshwater and marine food webs. Several reports have indicated a decrease in PFOS levels over time in contrast to PFCA concentrations that have tended to increase in tissues of aquatic organisms at many locations. The detection of precursor metabolites and isomers has become more frequently reported in environmental assessments yielding important information on the sources and distribution of these contaminants. The integration of environmental/ecological characteristics (e.g., latitude/longitude, salinity, and/or trophic status at sampling locations) and biological variables (e.g., age, gender, life cycle, migration, diet composition, growth rate, food chain length, metabolism, and elimination) are essential elements in order to adequately study the environmental fate and distribution of PFCs and should be more frequently considered in study design.