Estuaries are important ecosystems which are affected by a large range of environmental factors. It is important to measure, characterise and monitor the ecological status of estuaries, and this is the contribution of this thesis for phytoplankton communities in Southampton Water. The size structure and species composition were investigated during 2002 and 2003, with special attention to nanophytoplankton (cells < 5µm in diameter). The main sampling stations were Empress Dock and NW Netley in both years, and Calshot and Horse Elbow in 2002 only. To aid the interpretation of phytoplankton data, information about prevailing meteorological (air temperature, rainfall, irradiance) and hydrographic (tides, water temperature, salinity, and levels of inorganic nutrients) conditions were also collected. In 2002, Empress Dock was sampled weekly between February and October, and other stations were sampled monthly between May and October. In 2003, Dock and NW Netley were sampled weekly between April and September. Measurements made on the phytoplankton included size fractionated (<2, 2-5, 5-20, >20µm) chlorophyll, photosynthetic pigments by HPLC, cell counts by inverted microscopy, and in year 2003 flow cytometry counts and primary productivity (by oxygen) and Fast Repetition Rate Fluorometer (FRRF). Analyses of the major nanophytoplankton taxa involved oligonucleotide probes using fluorescent in situ hybridization (FISH) techniques. Plymouth Routines in Multivariate Ecological Research (PRIMER) statistical analyses were used to calibrate the environmental parameters and phytoplankton carbon biomass. The phytoplankton populations at the four stations were relatively similar. Maximum values of chlorophyll (chl) and carbon biomass were observed between May and August in both years, with a late diatom bloom in 2002, and a mid summer bloom for various organisms. Phytoplankton (as chl or carbon biomass) distributions for 2002 and 2003 could be divided into four phases associated with irradiance and nutrient level. However, there were rapid chl fluctuations during summer due to different factors, such as water column irradiance, tidal range and flushing rate. PRIMER analyses showed that phytoplankton carbon biomass distribution was associated with seasonal patterns, related to light irradiance water column light attenuation, tidal range and nutrients (N and P). In addition, Si is related to phytoplankton succession, and P to size fraction. The nanophytoplankton generally contributed 35-40% of total chlorophyll and up to 60% in winter at the outer stations. Chlorophyll size fraction measurements at Empress Dock (2002) and NW Netley (2003) showed that increased chlorophyll values are generally associated with fractions greater than 5µm (>5µm) and vice versa, although nanophytoplankton (carbon biomass) size structure was dominated by size 2-5µm followed by picophytoplankton, and flagellates >5µm became important in some samples. Comparison of total and fractionated pigment indicated that chlb and chlc2+3 were highly related to the nanophytoplankton fraction and probably inductive of the importance of Chlorophyta and Chrysophyta.