Pigments form a chemotaxonomic system widely used to determine phytoplankton composition and reconstruct water body histories by using sedimentary pigments as biological archives. This chapter presents protocols for pigment extraction from water and sediment samples. It also describes a method to separate, identify, and quantify major phytoplankton pigments in a single run. The method is based on high performance liquid chromatography with diode array detection (HPLC-DAD).