Increased topographic complexity has been linked to increased species diversity and/or abundance in many ecological communities, including coral reefs. Several topographic metrics can be measured remotely in GIS using high resolution bathymetry, including elevation, surface rugosity, and seafloor volume within specified areas. Statistical relationships between these data and organismal distributions within mapped habitats can be used to make predictions across the entire bathymetric dataset. In this study a model framework is presented which utilizes statistically significant relationships between reef fish abundance and species richness and GIS topographic complexity measurements for samples within similar benthic habitats to create GIS-based prediction maps of abundance and species richness for the entire seascape. Reef fish associations with GIS topographic metrics were significant and varied between habitats. Model evaluation showed that patterns in the measured data emerged in the prediction data. The results allow for viewing of data trends throughout the seascape, quantification of assemblages in non-sampled areas, and statistical comparisons of areas within the region to support and guide management related decisions. This model framework can be adapted to other communities (e.g. benthic organisms) and/or parameters (e.g. diversity) that relate to topographic complexity.