The sustainable management of coastal and offshore ecosystems, such as coral reef environments, requires the collection of accurate data across various temporal and spatial scales. Accordingly, monitoring systems are seen as central tools for ecosystem-based environmental management, helping on one hand to accurately describe the water column and substrate biophysical properties, and on the other hand to correctly steer sustainability policies by providing timely and useful information to decision-makers. A robust and intelligent sensor network that can adjust and be adapted to different and changing environmental or management demands would revolutionize our capacity to wove accurately model, predict, and manage human impacts on our coastal, marine, and other environments. Underwater measurements are greatly influenced by environmental conditions; especially in shallow waters. Temperature, salinity, turbidity, oxygen, pH and many other parameters still need optimization due to the difficulty in performing the process in situ in such an environment. Notably however, modern developments in wireless network technology and miniaturization now make it possible to realistically monitor the aquatic environment in situ using smart devices that are completely autonomous. However, to successfully use these kinds of systems in under water environments it is necessary from the outset to define the specific requirements and relative hindrances that such a field imposes; especially in terms of underwater information exchange. The aim of this paper is to examine these issues and to propose strategies for the cost effective and scientifically robust integration of remote sensor network technologies for the monitoring and management of critical marine environments such as coral reefs.