Perfluorinated compounds are industrial chemicals widely used for more than 60 years. However, during the last decade, due to their high resistance to degradation, bioaccumulation attached to proteins, biomagnification to the food chain and their relation to toxicological effects of these compounds have gained scientific and regulatory attention.In addition, the difficulty associated with their analysis in complex matrices such as biota, food and human fluids and tissues samples should be mentioned.This chapter provides a comprehensive examination of the current knowledge on PFCs' analysis, environmental fate and occurrence in aquatic systems, using as a central example the Llobregat River.