We collected high-resolution seismic reflection profiles in the southern part of San Francisco Bay in 1992 and 1993 to investigate possible Holocene faulting along postulated transbay bedrock fault zones. The initial analog records show apparent offsets of reflection packages along sharp vertical boundaries. These records were originally interpreted as showing a complex series of faults along closely spaced, sharp vertical boundaries in the upper 10 m (0.013 s two-way travel time) of Holocene bay mud. A subsequent survey in 1994 was run with a different seismic reflection system, which utilized a higher power source. This second system generated records with deeper penetration (max. 20 m, 0.026 s two-way travel time) and demonstrated that the reflections originally interpreted as fault offsets by faulting were actually laterally continuous reflection horizons. The pitfall in the original interpretations was caused by lateral variations in the amplitude brightness of reflection events, coupled with a long (greater than 15 ms) source signature of the low-power system. These effects combined to show apparent offsets of reflection packages along sharp vertical boundaries. These boundaries, as shown by the second system, in fact occur where the reflection amplitude diminishes abruptly on laterally continuous reflection events. This striking lateral variation in reflection amplitude is attributable to the localized presence of biogenic(?) gas.