Worldwide, marine protected areas (MPAs) are increasingly created to protect and restore selected parts of the ocean and to enhance recreation, fishing, and sustainable resources. However, this process has outpaced the development and implementation of methods for assessing and monitoring these habitats. Here, we combine data from an echosounder, a conductivity-temperature-depth probe, and underwater cameras to efficiently survey El Bajo Espíritu Santo Seamount, located in the southwest Gulf of California, Mexico. Results include a bathymetric map detailing a ridge with three peaks; oceanographic profiles showing a 35 m deep mixed layer and anoxic conditions below 200 m; mean target strength estimates for Pacific creolefish, Paranthias colonus (–34.8 dB re 1 m2, for mean total length ~33 cm), and finescale triggerfish, Balistes polylepis (–39.8 dB re 1 m2, 38 cm); baseline estimates of biomass for both species (55.7 t, 95% CI = 30.3–81.2 t and 38.9 t, 95% CI = 21.1–56.6 t, respectively) found only in the oxygenated water near the top of the seamount; and indications that these reef fishes grazed on zooplankton in the mixed layer. We conclude that acoustic-optical sampling is a practical approach for obtaining baseline information on MPAs to efficiently monitor changes resulting from natural and anthropogenic processes.