Surprisingly little is known about underwater marine environments and ecosystems owing to several factors. One important factor has been the general inability to observe and monitor these massive subsurface ocean spaces. Despite significant advances in sensor, communication and computing technology, underwater sensor platforms are generally inferior to their terrestrial counterparts. Here we highlight several sensor platforms that are currently being used and developed for underwater monitoring applications. We focus on two monitoring applications: 1) observation of whale sharks (Rhincodon typus); and 2) transport, accumulation and dispersion of plankton. In both cases, we describe the need for multimodal underwater sensor platforms to work in a cyber-physical mode, communicating a variety of different sensor data among them systematically to maximize acquisition of data. We think that this will substantially enhance understanding underwater ecosystems.