A robust and flexible technique to segment seafloor acoustic mapping data by analyzing co-located bathymetric digital elevation models and acoustic backscatter mosaics is presented. The algorithm first uses principles of topographic openness, pattern recognition, and texture classification to identify geomorphic elements of the seafloor or “area kernels”, and then derives the final seafloor segmentation by merging or splitting the kernels based on principles of similarity and multi-modality. The output is a collection of homogeneous, non-overlapping seafloor segments of consistent morphology and acoustic backscatter texture. Each labeled segment is enriched by a list of derived, physically-meaningful attributes that can be used for subsequent task-specific analysis.