Environmental pollution by organic compounds and metals became extensive as mining and industrial activities increased in the 19th century and have intensified since then. Environmental pollutants originating from diverse anthropogenic sources have been known to possess adverse values capable of degrading the ecological integrity of marine environment. The consequences of anthropogenic contamination of marine environments have been ignored or poorly characterized with the possible exception of coastal and estuarine waters close to sewage outlets. Monitoring the impact of pollutants on aquatic life forms is challenging due to the differential sensitivities of organisms to a given pollutant, and the inability to assess the long-term effects of persistent pollutants on the ecosystem as they are bio-accumulated at higher trophic levels. Marine microalgae are particularly promising indicator species for organic and inorganic pollutants since they are typically the most abundant life forms in aquatic environments and occupy the base of the food chain. We review the effects of pollutants on the cellular biochemistry of microalgae and the biochemical mechanisms that microalgae use to detoxify or modify pollutants. In addition, we evaluate the potential uses of microalgae as bioindicator species as an early sentinel in polluted sites.