From January to December 1999 (excepting July) the characterization of soft bottom macrobenthic fauna was performed in four different areas of Gorgona Natural National Park: Punta Brava, Yundigua, El Remanso, and La Mancora. Eight samples were taken at depths from 5 to 15 m using a PVC cylinder with an inner diameter of 15 cm and buried 10 cm into the seabed. Abundance, wet biomass, and organism composition were determinated. Organisms were identified up to family level. Univariate and multivariate statistical techniques allowed to define and characterize spatially and temporally the community to examine levels of disturbance and to relate the biological pattern to environmental variables of sediment and deep water. Significant differences (p < 0.05) between El Remanso and other sampled areas were found due to the higher value of abundance and richness in El Remanso but with no differences in family composition. Clustering and ordination showed changes in the community between January-June and August-December caused by differences in family composition and reduced richness and organisms abundance in the second semester, when ABC curves showed a polluted community. In the same way, mud and organic matter values in the sediment diminished in August-December, but total carbonates and water transparency increased. Granules and muds were the variable best correlated (rρ = 0.327, p < 0.01) to macrofauna distribution and structure, but other environmental factors may show stronger affinities to the community.