A two year survey (2000-2001) of the coastal Fleet lagoon, in Dorset, UK was performed with the aim of identifying the environmental conditions influencing the occurrence of phytoplankton blooms. Measurements included phytoplankton species abundance, biomass and identification, chlorophyll-a concentration, high performance liquid chromatography (HPLC) determined pigment concentrations, nutrients, temperature, irradiance, salinity, and data from a local meteorological station. Multivariate statistical methods (MDS and cluster analysis) were used to study temporal and spatial changes in species and environmental conditions. The quantification of biotoxins responsible for paralytic shellfish poisoning (PSP) and diarrhetic shellfish poisoning (DSP) in shellfish samples acquired from the Fleet lagoon was performed during 2001. The Abbotsbury embayment, at the brackish water end of the lagoon presented high levels of phytoplankton biomass, pigments and nutrients and may be considered eutrophic, in contrast to conditions observed in the east Fleet. Blooms of cryptophytes were observed at Abbotsbury during spring in both years and were related to new nutrient inputs that occur during winter. A bloom of the planktonic dinoflagellate Prorocentrum micans was observed in late summer-autumn 2000. The balance between freshwater and marine inputs to the Fleet and suitable conditions of nutrients and temperature plus longer water retention times were important determinants of the P. micans blooms in the west Fleet. Two toxic dinoflagellate species isolated from the Fleet lagoon were studied using laboratory cultures; the epi-benthic Prorocentrum lima that causes DSP and the planktonic Alexandrium minutum, responsible for PSP. DSP toxins were quantified using liquid chromatography linked to mass spectrometry (LC/MS) and PSP toxins using HPLC.  HPLC determined pigment profiles and measurements of nitrate and phosphate concentrations in the growth media provided estimates of nutrient uptake rates.