Relationships between phytoplankton species composition and environmental factors were studied in open areas of the central and eastern Gulf of Finland in late summer 1993. The data was collected using unattended water sampling, as well as spatially and temporally frequent measurements on in vivo fluorescence of chlorophyll a, temperature and salinity on board a passenger ferry, which plied between Helsinki and St. Petersburg. The relative abundances of phytoplankton species, concentrations of nutrients (Tot-N, NO2-N+NO3-N, NH4-N, Tot-P, PO4-P, Si) and chlorophyll a were analysed from the water samples. The collected data set enabled the use of various statistical methods in order to explain the phytoplankton community structure in the study area. The multivariate analyses were carried out using SAS software procedures (GLM, CLUSTER, CANCORR). Variability in the phytoplankton community (biomass, species composition) was high, and this paper clearly demonstrates that valuable information regarding pelagial biological dynamics, connected to extreme values, will be lost if the data is incorrectly simplified.