In this paper, attempt has been made to study the physico-chemical parameters of coastal waters of Mangalore and Padubidri, Southwest coast of India with special reference to diatom diversity for a period of 9 months from September 2014 to May 2015. The air and water temperatures ranged from 24.1 to 28.90C and 25.7 to 32.30C respectively, light extinction coefficient varied from 0.31 to 1.48m, total suspended solids ranged between 32 and 164mg/l, pH varied from 7.36 to 8.49, salinity fluctuated from 15 to 35PSU, dissolved oxygen ranged from 4.08 to 7.76mg/l, ammonia varied from 0.78 to 20.32µg-at NH3-N/l, Concentrations of nutrients, viz., nitrite and nitrate ranged from 0.06 to 11.70µg-at NO2-N/l and 0.08 to 39.77µg-at NO3-N/l respectively, phosphate and silicate varied from 0.10 to 2.80µg-at PO4-P/l and 8.35 to 52.35µg-at SiO3-Si/l respectively were recorded. The total of 55 species belonging to 27 genera of diatoms was recorded from six stations. Water temperature, dissolved oxygen showed significant positive correlation with total diatom species number, species richness, evenness, diversity and abundance. Nutrients, salinity showed significant negative correlation with species richness and evenness. The species diversity of diatoms were high in bar mouth region of Nethravathi and Gurupur estuary and the single species dominated during pre-monsoon season could be due to deterioration of water quality.