Echinoderm remains in the sand-size fraction of tropical, shallow-water carbonates were investigated in order to correlate depositional environments, preservation potentials, distribution, and taphonomic signatures. Fifteen sediment bulk samples were collected from five different environments at Fernandez Bay, San Salvador Island, Bahamas. Studied environments include: (1) intertidal beach rock, (2) subtidal bedrock overgrown by algae, (3) a subtidal Sargassum meadow, (4) a subtidal patch reef, and (5) subtidal loose sands without vegetation. At least 50 echinoderm elements and or fragments were randomly sampled from the fractions of 125–250 µm, 250–500 µm, and 500–1000 µm, resulting in a total number of 2355 ossicles. The distribution and taphonomic signature of the remains were analyzed using exploratory data analyses. Echinoid remains decrease coincident with an increase in ophiuroid ossicles from shore to reef. Encrustation and bioerosion are rare in the sand-sized fraction, whereas fragmentation and abrasion are common traits observed in all environments. Within-environment variation is high, however, and only the analyses of further transects can assess the influence of variability along the shore. The combination of distribution patterns and taphonomic signatures, however, reveals trends to distinguish three depositional environments that are characterized by: (1) a high percentage of echinoid remains, and high fragmentation and abrasion levels; (2) high fragmentation and low abrasion values; and (3) a high percentage of ophiuroid remains, and intermediate values for both fragmentation and abrasion. These results can aid in future analyses and interpretation of ancient carbonate deposits.