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In recent decades we have witnessed human-induced alterations to coastal watersheds that caused or aggravated eutrophication problems in estuarine systems. Although eutrophication is a natural process in the aging of lakes and estuaries, human activities are greatly accelerating this phenomenon by increasing the rate at which nutrients and organic substances enter aquatic ecosystems from their surrounding watersheds. Despite there is a fundamental understanding of the processes that cause eutrophication we still need to develop new methods and indicators and improve others to detect incipient eutrophication in ecosystems, providing information before major changes in species composition and abundance take place. The need of reliable indicators that correlate estuarine changes with human pressures over time (urban, industrial, and agriculture) is essential to understand their dynamics and to ensure effective management of these ecosystems. This chapter aims to evaluate the relative utility of rooted macrophytes and chemical variables in assessing eutrophication of two Portuguese estuaries subjected to different degrees of anthropogenic inputs owing to varied human activities and soil uses on their watersheds. We also document nitrogen deposition history in each estuary. [ABSTRACT FROM AUTHOR]