This paper describes the unique natural communities and biodiversity of the upwelling coastal system along the Guajira peninsula in the southern Caribbean Sea. The Guajira peninsula has a small human population with limited infrastructure and limited opportunities for coastal research, yet its coastal upwelling system is unique in the Tropical Western Atlantic region. This report includes both field observations along with a review of literature on the biodiversity of coastal eastern Guajira. In addition, it identifies missing information on the coastal system that is key to its management and conservation. Mangrove wetlands along with submerged aquatic vegetation (SAV) communities in a combination of consolidated and unconsolidated shorelines (e.g., rocky shores, cliffs, and beaches) form unique habitats in eastern Guajira. The diversity of these habitats is illustrated with the Bahia Hondita marine lagoon, where critical nursery habitat for several commercial valuable and endangered fisheries species, including sharks and sea turtles, is observed. Less information is available on more cryptic fauna, invertebrates, and coastal plankton species. Several anthropogenic factors are threatening species diversity in coastal Guajira, including overgrazing, mining, and target-species overfishing. Additional threats, such as extreme weather events (e.g., storms and droughts) as well as changes in coastal water quality, are also impacting species. The protection of the Guajira’s biodiversity would depend on local communities’ governance and empowerment as well as law enforcement for mining and agriculture operations. Management plans can include reducing land-based sources of pollution and building coastal resilience for climate change.