Microalgae using a submersible fluorescence probe in water column (up to 100 m) were measured during the austral summer of 2006 (February) in Prydz Bay, East Antarctica (triangular-shaped embayment in the Indian sector of Southern Ocean). Concurrently, environmental parameters such as temperature, salinity and nitrogen (nitrate, ammonium, urea) uptake rates were measured. The concentration of phytoplankton is relatively high due to availability of high nutrients and low sea surface temperature. Phytoplankton community is dominated by diatoms whereas cryptophytes are in low concentration. The maximum concentration of total chlorophyll is 14.87 ${mu}g;L^{-1}$ and is attributed to upwelled subsurface winter water due to local wind forcing, availability of micro-nutrients and increased attenuation of photosynthetically available radiation (PAR). Concentration of blue-green algae is low compared to that of green algae because of low temperature. Comparatively high concentration of yellow substances is due to the influence of Antarctic melt-water whereas cryptophytes are low due to high salinity and mixed water column. Varied concentrations of phytoplankton at different times of Fluoroprobe measurements suggest that the coastal waters of Prydz Bay are influenced by changing sub-surface water temperature and salinity due to subsurface upwelling induced by local winds as also melting/freezing processes in late summer. The productivity is high in coastal water due to the input of macro as well as micro-nutrients.