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A rapid method to estimate the three-dimensional (3D) surface area (SA) of marine gorgonians and sponges from field measurements of colony height, diameter, and morphology was developed as an indicator of habitat availability for fish and invertebrates. Colony characteristics for sponges and gorgonians were compiled from field measurements, expert judgment, and taxonomic literature, and employed to generate 3D images using computer-aided design software. The images were used to test various statistical models and geometric surrogates that best estimated SA using only height and diameter measurements. A morphological classification system was devised using shapes and relative proportions of sponges and gorgonians which are commonly found in shallow waters (< 25 m depth) of the Central Western Atlantic Ocean. Regression models (linear, quadratic, or cubic) were found to be more robust than geometric surrogates, exhibiting greater accuracy at range extremes. Statistical models explained over 90% of the variation in SA and forecast errors of less than 20%. The best models for estimating SA are presented for eight sponge and nine gorgonian morphologies. Application of these methods with existing estimators for stony corals SA can be used as an indicator of structural habitat availability, which is an important ecosystem service of coral reefs.