Global degradation of coral reefs is reflected in the destruction of shelters in various environments and threatens the stability of marine ecosystems. Artificial shelters offer an alternative, but their design is challenging due to limited knowledge regarding the shelter characteristics preferences of desired inhabitants. Investigating these preferences is resource-intensive, particularly regarding small shelters that mimic natural reef condition. Further, fish abundance may be too low for statistical analysis in small shelters. We propose a method to characterize the species-specific shelter preferences using low-volume data. During a study conducted from January 2021 to April 2022, round clay artificial shelters (RAS) were deployed on an abandoned oil pier to examine a coral reef fish community. We recorded 92 species from 30 families; grouped them to systematically (families) and functionally (dietary group) classes. Grouping enabled examining each group’s preference while crossing these group preferences revealed species- specific preferences, that matched field observations. This approach proved effective in profiling the shelter preferences of 17 species while having limited resources. These profiles may latter allow the establishment of ecological-oriented artificial reefs.