Morphological studies of fish assemblages are a crucial aspect of ecology, as they can provide insight into functional roles and changes beyond taxonomically oriented approaches. In addition, depth is an important factor that impacts the structure of fish assemblages. In the present study, samples of 115 demersal actinopterygian species were collected during a bottom-trawl survey conducted in the northern Aegean Sea, in the summer of 2020. The samples were collected by 65 hauls across depths ranging from 0 to 650 m. The samples were photographed, and the images were analyzed through geometric morphometric methods, by defining 27 landmarks and semilandmarks on each photo. Principal Components were estimated to construct morphospaces and between group Principal Component Analysis was used to distribute the mean body shape of each assemblage along morphological axes. Ecological, taxonomic and morphological diversity indices were then computed for each haul, and the potential effects of depth on these indices were tested with Generalized Additive models. All indices were significantly affected by depth, except for species richness, on which the effect was marginally insignificant. Concerning the morphological diversity indices, morphological disparity indices, estimated with 2 different methods, as well as the ecomorphological diversity found to increase with depth, whereas morphological richness fluctuated. Next, Generalized Linear Models were employed to examine the variations in the morphological traits of the mean shape of each formed assemblage. The results indicated that assemblages distinguished into two groups, one inhabiting the continental shelf (<200 m), and the other the upper-medium slope (>200 m). Specifically, with increasing depth, fish converge towards an elongated body, with larger mouth and eyes, but smaller pectoral fin. The findings of this study, contribute to better understanding of the impact of depth on the ecological and morphological structure of demersal assemblages, and highlight the importance of morphological diversity indices as a complement to conventional approaches.