Accurate characterization of marsh elevation and landcover evolution is important for coastal management and conservation. This research proposes a novel unsupervised clustering method specifically developed for segmenting dense terrestrial laser scanning (TLS) data in coastal marsh environments. The framework implements unsupervised clustering with the well-known K-means algorithm by applying an optimization to determine the “k” clusters. The fundamental idea behind this novel framework is the application of multi-scale voxel representation of 3D space to create a set of features that characterizes the local complexity and geometry of the terrain. A combination of point- and voxel-generated features are utilized to segment 3D point clouds into homogenous groups in order to study surface changes and vegetation cover. Results suggest that the combination of point and voxel features represent the dataset well. The developed method compresses millions of 3D points representing the complex marsh environment into eight distinct clusters representing different landcover: tidal flat, mangrove, low marsh to high marsh, upland, and power lines. A quantitative assessment of the automated delineation of the tidal flat areas shows acceptable results considering the proposed method is unsupervised with no training data. Clustering results based on K-means are also compared to results based on the Self Organizing Map (SOM) clustering algorithm. Results demonstrate that the developed multi-scale voxelization approach and representative feature set are transferrable to other clustering algorithms, thereby providing an unsupervised framework for intelligent scene segmentation of TLS point cloud data in marshes.