Observational evidence on an anomalous low saline pool due to excess rainfall and runoff during September 2020 in the South Eastern Arabian Sea (SEAS) is explained based on in-situ and satellite/reanalysis datasets. The study shows the presence of a low saline pool in the coast to offshore section between 10 and 14°N, which is associated with weak winds (3–5 m/s) and surface currents (0.1–0.2 m/s), compared to the long-term average. The pool is observed with strong vertical temperature gradient of 4°C and salinity gradient of 3.5 psu in the upper 20 m column. Cyclonic eddy in the central SEAS influences the distribution of low saline pool which suppress the coastal upwelling in the region. However, active upwelling is observed (surface temperature 6 m/s) and surface current (>0.2 m/s) which is also supported with weak rainfall and runoff. The high phytoplankton biomass in the nutrient-rich active upwelling region supports high zooplankton biomass. Contrastingly, the low saline pool region experienced low nitrate and phosphate concentration resulting into less chlorophyll concentration and that might be a plausible reason for the low zooplankton biomass.