There is still much to learn about ocean ecosystems. Long-term, continuous observations of underwater environments can help improve our understanding. This is especially important as we continue to develop ocean energy resources. The Pacific Northwest National Laboratory (PNNL) and the University of Washington have developed a real-time processing system for sonar to detect and track animals, and to extract water column biomass statistics in order to facilitate continuous monitoring of an underwater environment. The Nekton Interaction Monitoring System (NIMS) is built to continuously process in real-time a stream of sonar data and archive tracking and biomass data, reducing the volume of stored data by orders of magnitude. The prototype system has been tested for real-time performance in the laboratory and in an operational environment on-board a research vessel and as part of a multi-instrument monitoring system. NIMS currently works with three types of sonar: a multi-beam sonar, a split-beam echo sounder and an acoustic camera.