The small-sized copepod community structure (<1 mm) and its response to environmental variability was examined during an annual cycle in Kalloni Gulf, a semi-enclosed coastal system in the NE Aegean Sea. Α 90 µm net was used in order to adequately sample the smaller copepod fractions. In the copepod ecology the spatial patterns dominated over the seasonal. Total copepod abundance increased towards the inner gulf area while diversity indices followed the opposite trend. The inner gulf copepod assemblage area was affected by the increasing magnitude of eutrophication, characterized by high abundance values, low species richness and dominance of a single species (e.g. Oithona nana). A clear seasonal succession of species was observed, ordered by temperature, salinity, chlorophyll a, heterotrophic bacterial biomass, organic and inorganic nutrients. Freshwater inputs and the subsequent nutrient inflow was a dominant phenomenon enhancing copepod production and negatively affecting the biodiversity of the assemblage. The great contribution of copepod larval stages in the total community and their year-round presence indicate the continuous production of copepods during the annual cycle, highlight the importance of the smaller size fraction and encourage the use of finer mesh-size nets when assessing the structure and dynamics of copepod communities.