Mobile autonomous platforms are revolutionizing our understanding of ocean systems by providing a solution for the four-dimensional observation problem faced in the ocean. The sensors commonly used in autonomous platforms, however, leave a large gap in our observations of the food chain between primary producers and large predators. Echosounders have the potential to fill this gap. Here, we present details of a new, commercially available quantitative scientific echosounder specifically designed to meet the challenges of deployment in autonomous platforms, including those of relatively low power and small size, while providing data comparable to systems deployed from ships. We detail the integration into a Slocum glider of this echosounder and both upwardand downward-looking transducers to provide guidance for those considering similar efforts. We also identify key features of the system and the challenges that must be overcome to ensure collection of high-quality data. The most important feature of the integrated glider is that it carries instruments capable of providing depth profiles of bio-optical and environmental variables that are synoptic with the echosounder data. On a dive-by-dive basis, we can use these co-located data to quantify relationships between the acoustic, bio-optical, and environmental data. A field deployment of the echosounder-equipped glider elucidated the processes driving diel migration in zooplankton and nekton in Monterey Bay, emphasizing the novel science questions that can be addressed using contemporary means of accessing the sea and new, integrated tools for describing the habitat and its inhabitants.