*2.1. Geographic Setting*

The geographic focus of this paper is the upper portion of the San Francisco Estuary, including Suisun Bay, the Delta, and the Central Valley watershed upstream of the estuary (Figure 1). The Delta is the entry point of over 90% of the freshwater flow to the estuary [28] and drains the Sierra Nevada mountain range and Central Valley—a watershed of approximately 75,000 square miles. The configuration of the estuary formed approximately 5000 years ago when sea level rise stabilized [29]. Sea level rise maintained an average rate of 1.0–1.3 mm/yr [30] through the late Holocene until the late 19th century when it shifted to an average rate of 2 mm/yr [31].
