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The goal of this study was to consider the effects of habitat type and environmental conditions on the biodiversity of fishes within the Aransas Bay Complex, Texas and provide a management framework and an ecosystem examination of Essential Fish Habitat (EFH). A stratified, randomized experimental design was used to collect fishes from seagrass, oyster, and non-vegetated habitats within the Aransas Bay Complex from February through May 2010 over large spatial scales at the "bay-complex" level. We developed a biodiversity habitat model using Boosted Regression Trees (BRT). Fitted functions from the "best" fit BRT habitat model indicated that fish biodiversity was greatest in seagrass areas closest to the inlet (< 80 cost-distance units) during early spring, with temperatures < 18°C and dissolved oxygen levels between 7-8 mg O 2 /L in shallow depths (< 0.5 m). Results from community assemblage analyses showed significant differences among habitats with highest abundance of fishes found in seagrass, followed by non-vegetated substrate, and oyster reef. The relatively high abundance of fishes at non-vegetated bottom compared to the low abundance found at the oyster reef was most likely due to the spatial location of the habitats sampled. Our results indicate that future conservation measures should focus along the eastern and southern areas of Aransas Bay to protect EFH with highest levels of biodiversity. The modeling approach developed in this study provides a framework for natural resource managers to identify habitats supporting the greatest biodiversity of juvenile fishes.