The Water Framework Directive (WFD) requires the assessment of ecological quality of water bodies based on physico-chemical and biological elements. This paper is focused on the use of phytoplankton as a biological indicator of ecological quality in Portuguese transitional waters (TWs). Phytoplankton is considered to be a sensitive indicator to environmental changes, especially nutrient enrichment, and is therefore useful for evaluating eutrophication processes. According to the WFD, three metrics should be generally considered to assess ecological status: phytoplankton biomass (chlorophyll a), phytoplankton composition and abundance, and phytoplankton bloom intensity and frequency.This work presents an integrated methodology that comprises the first and the last metrics indicated above, analyzed during the growing season (February–October). Significant (p