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The relationship between nutrients and phytoplankton dynamics was investigated daily from 12 April to 22 July 2003 in Sagami Bay, Japan. According to multidimensional scaling (MDS) and cluster analysis, phytoplankton community was divided into four distinct groups. The first group was consisted of centric diatom species, such as Guinardia spp., Detonula spp., Letocylindrus danicus, Skeletonema costatum, Eucampia zodiacus and Chaetoceros spp.. The second and third clusters comprised mainly diatoms and dinoflagellates, respectively. The other cluster was restricted to the samples collected during the last sampling period when the rainfall and river discharge was frequently recorded. Canonical correspondence analysis (CCA) was applied to analyze four groups respectively, which focused on the effects of nutrients concentration and ratio on phytoplankton variations. Based on CCA analysis, most species of centric diatom were negatively correlated with DSi concentrations and Si/N ratio. Nutrients were strongly limited phytoplankton growth during the summer when the rainfall was not observed, whereas river discharge by rainfall and counterclockwise coastal currents (although the surface circulation pattern is often altered by Kuroshio Current, the counterclockwise coastal currents are generally dominant) has brought phytoplankton population accumulation and triggered the micoalgae growth in western part of the bay. Phosphorous (P) was strongly limited after significantly increases in the phytoplankton abundances. However, silicate (Si) was not a major limiting factor for phytoplankton production, since Si/DIN and Si/P ratio did not create any potential stoichiometric limitation. This indicates that high Si availability contributes favorably to the maintenance of diatom ecosystems in Sagami Bay.