Oceans cover most of the planet and 60% of the world's population lives near the coast. Anthropogenic activities along coastlines and in the open ocean have placed the oceans in peril. According to a Pew Oceans Commission Report, among the greatest threats to the ocean are land-based runoff from coastal development, nutrient pollution, overfishing, and invasive species. Here, we describe threats due to microbial, nutrient, chemical, and plastic pollution in addition to declining biodiversity and describe fundamental and applied research needed to mitigate the threats. While the research needs are diverse, we identify several research foci that transcend individual threats: monitoring, fate and transport studies, modeling, innovative natural and engineered treatment systems, and toxicity and health studies. Research within the environmental engineering and science community that addresses these needs will contribute to improving ocean health.