As an intermediary connection between primary producers and higher trophic levels, zooplankton are an important component of the aquatic food chain, contributing significantly to aquatic biological productivity. This study describes the zooplankton diversity and community structure, as well as their relationships with ecological factors, in homestead ponds of a coastal district along the northern Bay of Bengal region. Significant differences (p < 0.05) were detected in the mean values of temperature, pH, DO, TDS, transparency, and phosphates from the ponds during December 2020, but no significant differences were found in the nitrate levels. However, no significant variances in the ecological parameters between months were found due to the study taking place in the same season. Sixteen zooplankton species, representing four groups, were found in the study area, with the highest mean abundance of 301.19 ± 40.55 ind./L recorded in February 2021 and the lowest of 293.02 ± 21.13 ind./L recorded in December 2020. The diversity (H’), evenness (e), richness (J), and dominance (D) ranged from 2.49 to 2.12, from 0.93 to 0.84, from 2.05 to 1.56, and from 0.13 to 0.09, respectively. Based on the SIMPER analysis, Diaptomus gracilis and Brachionus calyciflorus were found to be significant contributors (>10%) to the zooplankton community structure in different months. The ANOSIM results revealed that 10 species of zooplankton were significant contributors based on their average dissimilarity. The canonical correspondence analysis (CCA) identified that pH, transparency, nitrates, and phosphates have a significant impact on the abundance of zooplankton species in the homestead ponds in the study area.