<p>The effects of different substrates on zooplankton diversity and functional composition in integrated multitrophic aquaculture (IMTA) systems are insufficiently understood. This study aimed to evaluate the influence of the substrates geotextile blanket (GB) and bamboo (BAM), and water physical and chemical variables on zooplankton diversity and functional composition in IMTA ponds. A totally randomized designed experiment with three treatments (two substrates and no substrate) and four replicates (earthen ponds) were performed. All ponds were stocked with Nile tilapia and Amazon river prawn. Zooplankton were characterized based on body size, feeding type, trophic group, and habitat preference. Functional diversity indices (Functional Richness — FRic, Functional Evenness — FEve, Functional Dispersion — FDis, and Functional Divergence — FDiv) were calculated and modeled using generalized linear mixed models considering substrates and water parameters. Physical and chemical variables included dissolved oxygen (DO), pH, electrical conductivity, temperature, transparency, total nitrogen (TN), total phosphorus (TP), total suspended solids (TSS), and chlorophyll <i>a</i>. Results indicated only FDis was higher in CON treatment than others. Substrates also affected trophic group distribution, with BAM promoting herbivores-detritivores organisms due to increased pond structural complexity. FRic was highest in ponds with neutral pH and low TSS; FEve was highest in high conductivity and low TP ponds; FDis was highest in ponds with high TSS and TP; and FDiv was highest in high conductivity ponds. Functional trait categories showed complex associations with electrical conductivity, which was identified as the key variable influencing zooplankton community structure.</p>