"Historically, we thought (the Sacramento and San Joaquin) were the dominant inputs of contaminants in the bay, but our thinking has shifted," Davis said. "The tributaries from the urban landscapes are contributing more."

Read more: http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2010/10/04/BAPC1FO6QP.D...

This article explains how urban areas are a bigger threat to the Bay than the farmlands of the Central Valley. Jay Davis is quoted in this article