Coastal wetlands, such as mangroves, seagrass beds, and salt marshes, are highly threatened by increasing anthropic pressures, including chemical pollution. Persistent organic pollutants (POPs) have attracted attention in these particularly vulnerable ecosystems, due to their bioaccumulative, pervasive, and ecotoxic behavior. This article reviews and summarizes available information regarding current levels, biogeochemical cycling, and effects of POPs on coastal wetlands. Sediment POP levels were compared with international quality guidelines, revealing many areas where compounds could cause damage to biota. Despite this, toxicological studies on some coastal wetland plants and microorganisms showed a high tolerance to those levels. These taxonomic groups are likely to play a key role in the cycling of the POPs, with an active role in their accumulation, immobilization, and degradation. Toxicity and biogeochemical processes varied markedly along three main axes; namely species, environmental conditions, and type of pollutant. While more focused research on newly and unintentionally produced POPs is needed, mainly in salt marshes and seagrass beds, with the information available so far, the environmental behavior, spatial distribution, and toxicity level of the studied POPs showed similar patterns across the three studied ecosystems.