Coral reefs exposed to nitrate and phosphate enrichment can contribute to coral degradation by promoting competitive growth and altering coral holobiont performance. Although the relationship between nutrients and coral reefs has been studied, few studies have linked them to discovering possible nutrient sources and their impacts on coral reefs. To address this gap, an overview was presented to discuss possible nutrient sources that may contribute to the nitrate and phosphate enrichment in coral reefs of Southeast Asian waters and their impact on coral health in Malaysia. As a result of these anthropogenic activities, it has been published that most Indonesian reefs experienced high concentrations of nitrate and phosphate, while reefs in Singapore were the least affected. Only 12 study sites in Malaysia found that nitrate and phosphate enrichment could affect sea anemones, sea urchins, and macro- and microalgae growth, as well as the increased coral disease prevalence and decreased coral recruitment rate, eventually leaving most corals in fair to poor health.