Collecting detailed surveys of the environmental and biological distributions in the epipelagic and mesopelagic ocean is important for understanding the basic processes that govern these expansive habitats and influence the earth system at large. Common ocean sampling platforms (e.g., net systems, moored, and shipboard sensors), are often unable to resolve marine biota at scales comparable to the variability associated with their own behavior or that of their physical environment. Newer approaches using mobile robotic systems carrying multiple environmental sensors have enabled detailed interrogation of the fine and sub-mesoscale distribution of animals and have provided more context for the water column structure. We integrated a dual-frequency broadband split-beam echosounder (Simrad EK80 with 70 and 200 kHz transducers) into the Wire Flyer profiling vehicle to achieve concurrent hydrographic and acoustic sections in the midwater environment (0-1000 m) at novel scales. The Wire Flyer provides high-resolution repeat profiling (0-2.5 m s À1 up and down velocity) within specified water column depth bands typically spanning 300-400 m. This system can provide acoustic backscatter data at depths unavailable to shipboard surveys due to attenuation limits and can be operated in tandem with conventional shipboard echosounders to provide overlapping acoustic coverage with concurrent hydrographic sections. The side-looking transducer orientation, as opposed to the traditional vertically oriented arrangement on ships, samples orthogonal to the vehicle's profiling survey path and provides a direct measurement of animal distributions in the horizontal. The processed data have demonstrated the system's capacity to track migrating layers and resolve coherent biological patches and single targets in the horizontal, rising seafloor gas plumes, and scattering layer distributions tightly coupled to measured sub-mesoscale features such as strong vertical oxygen gradients.