Estuaries are coastal indentations where freshwater mixes with seawater (Pritchard 1967), and are found everywhere in the world. Moreover, the estuarine ecosystems are usually characterized by high biological productivity and great biodiversity. However, these characteristics are very sensitive to the climate regime, the geological environment and the hydrological quality. In metropolitan environments with high social, urban and economic complexity, river flows usually play an important role in the regulation of estuary biochemistry, and therefore their control is essential.