Zeinab, the U.S. Environmental Protections Agency has protocols and guidelines for watershed assessment. You might want to start by visiting this web page: http://water.epa.gov/polwaste/nps/watershed/examples.cfm
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Rapport, D. J., Costanza, R., & McMichael, A. J. (1998). Assessing ecosystem health. Trends in Ecology & Evolution, 13(10), 397-402.
You can study abbsolutly and trend health I think.
Controling input and output of watershed system in sediment, water and vegetation balance can be usefull for this control. It can be multi temporal for trend study.