Terrestrial and aquatic environments are deeply connected through the transfer of nutrients, contaminants, and energy across landscapes. This chapter outlines how the major biogeochemical cycles of nitrogen, phosphorus, and carbon function within aquatic systems and describes the microbial and ecological processes that maintain these cycles. It further explains how human-driven inputs—such as agricultural runoff, industrial discharges, untreated sewage, and emerging pollutants including PFAS, pharmaceuticals, heavy metals, and microplastics—disturb natural processes. Once introduced into water bodies, these contaminants undergo various transformations that influence their mobility and lead to bioaccumulation and biomagnification, posing serious risks to aquatic life, fisheries, aquaculture, and human well-being. The chapter also examines how pollution reduces aquaculture performance, heightens disease occurrence, and creates challenges for meeting global seafood safety standards. It discusses a range of sustainable interventions, including advanced wastewater treatment, environmentally friendly farming practices, clean industrial technologies, and nature-based restoration solutions. Modern monitoring tools—such as remote sensing, GIS, biosensors, and automated water-quality systems—are presented as essential for timely detection and management of pollution. Governance mechanisms, including the Sustainable Development Goals, international environmental agreements, and integrated coastal and ecosystem-based management approaches, support coordinated action across land–sea boundaries. With climate change altering pollutant pathways and intensifying ecological stress, the chapter emphasizes the need for integrated strategies rooted in a One Health framework. Addressing remaining knowledge gaps, particularly concerning emerging contaminants and their interactions with climate drivers, will require stronger scientific collaboration and improved data sharing. Ultimately, safeguarding aquatic ecosystems and securing global food supplies demand comprehensive, science-based, and inclusive management efforts.