The principal objectives of this study were to understand how hydrodynamic and biogeochemical processes interact to produce reductions in dissolved oxygen concentrations in the Stockton Deep Water Ship Channel (DWSC) and to produce a three-dimensional hydrodynamic and coupled water quality model that could be used to examine these interactions. To address these objectives, an ambitious program of field experimentation and numerical model development was undertaken. The collaboration included UC Davis, Stanford University, the US Geological Survey, the University of Granada (Spain), UC Santa Barbara and the Lamont-Doherty Earth Observatory at Columbia University. The individual program elements were the subject of individual reports that were submitted and subsequently accepted by CBDA. This final report primarily collates these individual reports and the peer-reviewed publications that stemmed from them, into a single final report.