Fish monitoring gears rarely capture all available fish, an inherent bias in monitoring programs referred to as catchability. Catchability is a source of bias that can be affected by numerous aspects of gear deployment (e.g., deployment speed, mesh size, and avoidance behavior). Thus, care must be taken when multiple surveys—especially those using different sampling methods—are combined to answer spatio-temporal questions about population and community dynamics. We assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary: the Bay Study Otter Trawl (BSOT), the Bay Study Midwater Trawl (BSMT), the Fall Midwater Trawl (FMWT), and the Suisun Marsh Otter Trawl (SMOT). We used generalized additive models with a spatio-temporal smoother and survey as a fixed effect to predict gear-specific estimates of catch for 45 different fish species within large and small size classes. We used estimates of the fixed effect coefficients for each survey (e.g., BSOT) relative to the reference gear (FMWT) to develop relative measures of catchability among taxa, surveys, and fish-size classes, termed the catch-ratio. We found higher relative catchability of 27%, 22%, and 57% of fish species in large size classes from the FMWT than in the BSMT, BSOT, or SMOT, respectively. In the small size class, relative catchability was higher in the FMWT than the BSMT, BSOT, or SMOT for 50%, 18%, and 25% of fish species, respectively. As expected, relative catchability of demersal species was higher in the otter trawls (BSOT, SMOT) while relative catchability of pelagic species was higher in the midwater trawls (FMWT, BSMT). Our results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.