Biolog plates were used to study the changes in the metabolic capabilities of bacterioplankton over a complete tidal cycle in a tropical ecosystem (Cochin Estuary, Kerala, India) along southwest coast of India. The pattern of utilization of carbon sources showed a definite shift in the community metabolism along a salinity gradient. Multivariate statistical analysis revealed two communities, namely allochthonous bacterioplankton sensitive to salinity and autochthonous bacterioplankton, which are tolerant to wide salinity fluctuations. Regression analysis showed salinity as the most important parameter influencing the physiological profile of bacterioplankton, irrespective of tide. Apart from salinity, limno-tolerant retrievable counts and halo-tolerant retrievable counts also accounted for the metabolic variation of bacterioplankton during low and high tides, respectively. The shift in the substrate utilization from carbohydrates to amino acids appears to be due to the physiological adaptation or nitrogen limitation of bacterial community with increasing salinity.