Approximately 75% of the Earth’s surface is covered by water, and 78% of the global animal kingdom resides in marine environments. Furthermore, algae and microalgae in marine ecosystems contribute up to 75% of the planet’s oxygen supply, underscoring the critical need for conservation efforts. This review systematically evaluates the impact of underwater communication systems on aquatic ecosystems, focusing on both wired and wireless technologies. It highlights the applications of these systems in Internet of Underwater Things (IoUT), Underwater Wireless Sensor Networks (UWSNs), remote sensing, bathymetry, and tsunami warning systems, as well as their role in reducing the ecological footprint of human activities in aquatic environments. The main contributions of this work include: a benchmark of various underwater communication systems, comparing their advantages and limitations; an in-depth analysis of the adverse effects of anthropogenic emissions associated with communication systems on marine life; and a discussion of the potential for underwater communication technologies, such as remote sensing and passive monitoring, to aid in the preservation of biodiversity and the protection of fragile ecosystems.