For nearly 50 years, the California Department of Fish and Wildlife has used a midwater trawl to intensively monitor fish populations in the San Francisco Estuary during the fall, sampling over 100 locations each month. The data collected have been useful for calculating indices of fish abundance and for detecting and documenting the decline of the endangered fish species delta smelt (Hypomesus transpacificus). However, efforts to calculate estimates of absolute abundance have been hampered by the lack of information on gear efficiency, in particular questions about contact selectivity and the effect of tow method on catches. To answer these questions we conducted a study that used a covered cod end on a net towed either near the surface, referred to as a surface tow, or throughout the water column, referred to as an oblique tow. A contact selectivity model was fit to estimate the probability that a delta smelt that has come into contact with the net is retained in the cod end of the net conditional on its body length. Full retention of delta smelt was found to occur around 60 mm fork length. Delta smelt catch densities for the surface tows were an order of magnitude greater than densities in the oblique tows, suggesting a surface orientation at the sub-adult life stage. These results represent an important step in being able to calculate absolute abundance estimates of the delta smelt population size using decades’ worth of monitoring data.