Phytoplankton community composition and its relation to environmental conditions, provides a valuable bridge to understanding the spatio-temporal dynamics of this compartment and the population responses to significant variation in the driving constraints. The combination of pigment-based chemotaxonomy and inverted microscopy screening with the identification of dominant species have been proven to be a useful phytoplankton-monitoring tool in coastal ecosystems. Here, we present results from a study combining these methods to (i) evaluate the importance of pico- and nanophytoplankton compartments, imperceptible by optical microscopy and (ii) evaluate how phytoplankton functional groups may respond to environmental variations underlying coastal ecosystem changes, by assessing the key factors controlling phytoplankton dynamics and influencing the community structure. For this, phytoplankton microscopic enumerations and HPLC-DAD analyses of their pigments were performed on a fortnightly basis during two years at several coastal stations in the English Channel characterized by their contrasting abiotic environment. Pigment-based taxonomic groups were shown to reflect changes in phytoplankton community structure throughout time and space reflecting the complex interactions between functional groups and combination of key factors such as temperature, nutrient availability, salinity and probably grazing or parasite pressure. By using a statistical framework based on an ordination technique the community structure was analysed and interpreted in terms of niche marginality and tolerance. These results suggest that the combination of microscopic observations and pigment-based data may provide reasonable insights of changes in phytoplankton communities in response to multiple environmental stressors such as climate change or nutrient enrichment process.