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We present for the first time, data on fish assemblage structure for ten temporarily closed estuaries (TCEs) along the south-western coast of India. Fish community structure differed significantly between TCEs based on species presence/absence, estuarine use and feeding mode. Marine migrant and freshwater stragglers dominated the 'fish guilds', while piscivores and zoobenthivores were the major feeding guilds, in all estuaries. We used the Estuarine Fish Community Index (EFCI) and a Combined Anthropogenic Pressure Index (CPI) to determine the ecological quality of TCEs. The application of functional guilds and EFCI successfully represented the use of TCEs by fish communities, and also the functional similarities existing between fish assemblages of these estuaries, despite considerable taxonomic, physical and chemical differences. EFCI indicated that the ecological health of TCEs in south-western India ranges from 'poor' to 'good'. We also established a significant relationship between CPI, EFCI and ecological quality in various TCEs using the Generalized Linear Model (GLM). [ABSTRACT FROM AUTHOR]