Many aquatic ecosystems, such as lagoons or lakes, are increasingly vulnerable to climate changes and human pressure. The environmental and economic costs of anthropogenic eutrophication are high as well as the applied methods to counteract eutrophication This chapter analyzes the variation in abundance (and biomass) of several phytoplankton families in one of the most well-known volcanic lagoons in the Archipelago of the Azores-Portugal (Furnas Lagoon) and the dynamic correlation between groups of different types of algae that have been established seasonally between 2003 and 2018. For that purpose, the principal component analysis (PCA) technique was used in data series on biomass and abundance of phytoplankton and chlorophyll a, in the time interval considered. The application of PCA techniques in natural phytoplankton populations offers the possibility of making rapid qualitative diagnoses of the trophic state in natural lakes. On the other hand, the fluorescence properties of phytoplankton microorganisms are strongly affected by the physicochemical properties of natural waters. The fluorescence emission and the lifetime of the different water samples were obtained by photon counting with time correlation (TCSPC), allowing to establish the fluorescent signature of these phytoplankton groups under certain conditions.