Abstract Foraging profitability is one of the significant factors affecting habitat selection in fishes. The food habits of the fish species vary seasonally due to the dynamic nature of their environment. For that, the dietary analysis of a fish is essential in the case of fish diversity research. Most of the variations in prey size consumed by piscivores were correlated to the differences in piscivore body size, which morphological constraints can explain. The present study aimed to investigate the ecomorphological assemblage of small indigenous freshwater fish species from smaller lentic freshwater bodies based on a range of morphological traits and evaluate fish assemblages with respect to the feeding guilds. Freshwater ponds around Birbhum district, West Bengal (India) were selected for the collection of fish species, namely Amblypharyngodon mola, Puntius sophore, Esomus danrica, Lepidocephalichthys guntea, Chanda nama, Parambassis lala, Trichogaster fasciata, Anabas testudineus and Glossogobius giuris. Morphometric and gut content analysis were done, and the trophic guild matrix, taxonomic distance matrix, and morphological matrix were calculated. The result showed a strong association between ecomorphological traits and trophic structure, indicating an independent assemblage pattern beyond the taxonomic influence.