We surveyed two sites in the southern California continental borderland with a newly developed instrument, a towed deep ocean gravimeter—a gravity sensor that can be towed a few tens of meters above the sea floor. During its development phase, we used the instrument to survey two regions off the coast of southern California. The first was along two tracks in the San Diego Trough. The second was over a seamount-like feature named Emery Knoll. Results of the trough survey reveal a basin with a geometry consistent with seismic data. We observed no significant density contrast across the San Diego Trough fault in the near-surface sediments. The survey of Emery Knoll shed light on the question of the origin of this structure; modeling the knoll to determine its bulk density suggested a nearly uniform structure surrounded by sedimentary basins with a more massive central intrusive body. Derived densities of 2850 kg/m3 for the knoll and 3050 kg/m3 for the central intrusion assume that no deep unmodeled sources exist directly underneath the knoll. The gravity data favor a model of metamorphic basement rock uplifted and containing igneous intrusives.