A real-time, marine acoustic monitoring system and method for detecting, tracking, recording, analyzing, communicating and otherwise obtaining and manipulating data indicative of marine presence and/or activity, and using such data to avoid or mitigate detrimental impact on the marine environment. The system includes sub-sea instrumentation packages (SPs) including sensors recording acoustic signals and other sensor data that allow elapsed and/or real-time, in-situ data communications and control of the individual instrumentation packages and system configuration. Each SP may have wireless, acoustic, and/or optical modules or components to enable the communication between SPs and/or other collection points such as surface vessels, ROVs, sub-sea transceivers, or AUVs. The SPs may further include additional single or multi-component seismic or other functionalized sensors for collecting data that may be used in combination with acquired acoustic data (which may relate to environmental conditions as described below as well as to marine mammal acoustic data) to assist in the identification, localization, and/or changes in the characteristics and/or population(s) of mammals in the sensed environment or other stimuli such as, but not limited to, radiation, movement, and any other detectable stimuli of real or potential interest.