Historically, estuaries have been areas of settlement for many human populations, resulting in a number of negative effects on the natural environment. For example, land reclamation, harbour extension, and dredging lead to decreased areas of wetlands that are very important for the protection of water quality as well as their floristic and faunistic interest. Water quality in estuaries and particularly in urbanized regions is decreasing as a consequence of anthropogenic activities, namely inputs of chemicals associated with industrial and domestic activities and pesticides and fertilizers originating from agriculture. In addition to such local contamination, estuarine ecosystems are exposed to toxic anthropogenic effluents transported by rivers constituting the whole river basin. Concomitantly, river transport is responsible for influxes of nutrients that underlie the biological wealth of estuarine areas, ensuring their role as nurseries for many commercial species. River transport of nutrients is also responsible for the high productivity of nearby coastal areas, allowing the establishment of mariculture enterprises. However the concomitant influx of nutrients and contaminants is a source of concern related to the growth and reproduction of cultivated species and represents a health risk related to the quality of seafood products. Thus estuaries are crucial in the life histories of many invertebrates and vertebrates and the sustainability of estuarine biodiversity is vital to the ecological and economic health of coastal regions.