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There is a high demand for underwater communication systems due to the increase in current human underwater activities. Underwater communication systems employ either sonar or electromagnetic waves as a means of transferring signals. These waves are different physically and electrically, and thus the systems that employ them also differ in their design architecture, wave propagation and devices used for emission and reception. As a result, the two systems have varying advantages and limitations. This paper presents an in-depth review of underwater communication based on sonar and electromagnetic waves, a comparison of the two systems and a discussion of the environmental impacts of using these waves for underwater communication. In the tradeoff between preserving the underwater environment and the need for underwater communication, it appears that underwater electromagnetic wave communication has the most potential to be the environmentally-friendly system of the future.