In this chapter we review the effects of anthropogenically derived chemical pollutants on tropical coral reef ecosystems. A wide range of compounds, including pesticides, trace metals and petroleum hydrocarbons enter reef systems through various pathways and affect different reef species and/or life history stages. Tools for evaluation of chemical stress on coral reefs consist of molecular, biochemical, physiological and ecological bioindicators, providing information at organismal or community levels. This chapter collates and assesses available information on different chemical stressors in the marine environment and the effects on reef-building corals. Ecological effects from chemical stressors are strongly dependent on exposure characteristics. Three probable pollution scenarios are discussed and their individual properties evaluated. Short-term, pulse-like pollution events including oil spills or antifoulant deposition through ship groundings often have a direct and severe impact upon multiple trophic levels of the system. However, these events are typically localised and possibly irrelevant on an ecosystem-wide scale. In contrast, recurring pollution events such as input from river floods or chronic pollution from land runoff (e.g. sewage treatment effluent or herbicides), may exert subtle effects on lower trophic levels of the system, affecting species fitness and driving adaptation. Effects from recurring or chronic pollution are more likely to combine and interact with other environmental factors, but remain poorly understood. Over time, chronic sub-lethal stress may decrease resilience of reef organisms to other forms of environmental stress like elevated sea surface temperatures and ocean acidification.