Estuaries are among the most dynamic, complex, and biologically productive ecosystems in the world (Alongi 1998, Good 1999). Yet, they are also extremely vulnerable to human disturbance (Kennish 2002, Lotze et al. 2006). Large estuaries, such as the San Francisco Bay, are highly coveted places for human habitation, recreation, industry, and agriculture. Currently, over 7 million people live in the Bay Area (MTC-ABAG 2012), placing unprecedented pressures on the region’s biological resources, goods, and services.