High resolution remotely sensed bathymetric data is rapidly increasing in volume, but analyzing this data requires a mastery of a complex toolchain of disparate software, including computing derived measurements of the environment. Bathymetric gradients play a fundamental role in energy transport through the seascape. Benthic Terrain Modeler (BTM) uses bathymetric data to enable simple characterization of benthic biotic communities and geologic types, and produces a collection of key geomorphological variables known to affect marine ecosystems and processes. BTM has received continual improvements since its 2008 release; here we describe the tools and morphometrics BTM can produce, the research context which this enables, and we conclude with an example application using data from a protected reef in St. Croix, US Virgin Islands.Geosciences 2018, 8, 94 2 of 24 and better understanding of the algorithms in use, the field will lend itself more readily to expanding understanding of our oceans.Today, modern seafloor mapping technologies such as light detection and ranging (LiDAR) and multibeam bathymetry have done much to lower the costs, and provide consistent bathymetric products which incorporate in-sensor error models, provide high point density, and accurate georeferencing making them suitable for scientific analysis [10,11]. Bathymetric data are often captured, processed to remove artifacts and errors, and integrated into a consistent geomorphological model. Creation and interpretation of such a model has been aided by geomorphometry analysis tools in packages such as Benthic Terrain Modeler (BTM) [12,13]. BTM is built on top of the popular ArcGIS platform, is open source, has an intuitive interface, and has received continual development. When BTM was first introduced in 2006, transforming collected data to research results required mastery of many different pieces of software.Recent methodological developments have reduced the complexity of doing such analysis, but this has coincided with the emergence of even more sophisticated tools and the ability to collect much higher resolution data. Here, we describe the tools provided with the current release of BTM (v3.0), and highlight how it can be used in powerful analytical workflows for seafloor classification, by combining it with the capabilities of ArcGIS, the Python scientific stack, and the R statistical programming language. As the sphere of scientific software continues to grow, it will be important to provide easy-to-use tools to aid the broader community in performing rigorous analysis of marine geomorphometry.