ABSTRACT : Variations of total, size- fractioned chlorophyll a, species composition and abundance of phytoplankton in Southampton Water were investigated. The study included three segments of Southampton Water representing the different salinity points, Woodmill (freshwater), Northam (brackish water) and NW Netley (saline water). Factors that are responsible for the seasonal and temporal variations in chlorophyll a and species composition in Southampton water are diverse. Light, spring/ neap tidal cycles and nutrients seem to be overriding importance during the present study. The first part of the research project involved enumeration and identification of the groups present in the phytoplankton samples from the three sites collected at fortnightly intervals during spring and summer, 2003. The phytoplankton community of Southampton water showed differences in species composition and dominance between the two different seasons. The spring phytoplankton communities consisted mainly of diatoms while the summer was dominated by dinoflagellates and ultraphytoplankton. The biomass indicator, chlorophyll a showed three peak times during the sampling period. The maximum value of 32.9mg m-3 achieved at NW Netley during the first bloom period. Variations in the contribution of four size fractions (>20, 5-20, 2-5 and 0.2-2m) to the total phytoplankton chlorophyll a were investigated during spring- summer months. The present observations indicate that the >20m fraction followed by the 5-20m fraction were the most important fractions dominating the sampling stations The distribution of total chlorophyll a relative to salinity showed in most cases the existence of considerable horizontal variations. The chlorophyll a concentration increases in a seaward direction. The third part of this research was designed to determine the suitability of the new molecular method (Fluorescent In-Situ Hybridisation) combined with flow cytometry for the enumeration and identification of the small photosynthetic eukaryotes (ultraphytoplankton) that were difficult to be identified in many cases, using the light microscopy because of their small size and simple morophology. The results demonstrate that cells belonging to the division Chlorophytes and the group Haptophyta were dominant in all stations throughout the sampling time.