Long-term fish sampling data from the San Francisco Estuary were combined with detailed three dimensional hydrodynamic modeling to investigate the relationship between historical fish catch and hydrodynamic complexity. Delta Smelt catch data at 45 stations from the Fall Midwater Trawl (FMWT) survey in the vicinity of Suisun Bay were used to develop a quantitative catch-based station index. This index was used to rank stations based on historical Delta Smelt catch. The correlations between historical Delta Smelt catch and 35 quantitative metrics of environmental complexity were evaluated at each station. Eight metrics of environmental conditions were derived from FMWT data and 27 metrics were derived from model predictions at each FMWT station. To relate the station index to conceptual models of Delta Smelt habitat, the metrics were used to predict the station ranking based on the quantified environmental conditions. Salinity, current speed, and turbidity metrics were used to predict the relative ranking of each station for Delta Smelt catch. Including a measure of the current speed at each station improved predictions of the historical ranking for Delta Smelt catch relative to similar predictions made using only salinity and turbidity. Current speed was also found to be a better predictor of historical Delta Smelt catch than water depth. The quantitative approach developed using the FMWT data was validated using the Delta Smelt catch data from the San Francisco Bay Study. Complexity metrics in Suisun Bay were-evaluated during 2010 and 2011. This analysis indicated that a key to historical Delta Smelt catch is the overlap of low salinity, low maximum velocity, and low Secchi depth regions. This overlap occurred in Suisun Bay during 2011, and may have contributed to higher Delta Smelt abundance in 2011 than in 2010 when the favorable ranges of the metrics did not overlap in Suisun Bay.