The Hueneme Submarine Canyon's configuration is structurally controlled by the Hueneme Fault Zone that was mapped from UNOCAL's seismic line collection in the 1980's (U.S. Minerals Management Service, 1995-2002). The canyon depths were also mapped by the U.S. Department of Commerce in two nautical charts (2013) showing bathymetric contours interpreted as a steep canyon straight-line structure within the shipping channel that strikes N19°E, and meanders further offshore, measured at 2.9 km (1.8 mi) wide, and 14.8 km (9.2 mi) long. The canyon's flank walls contain varying slopes up to 35°. The canyon contains shallow to deep subsea depths that were sounded from 6 fathoms (36 feet) ranging up to 317 fathoms (1,902 feet).  At the farthest extent (end) of the canyon, the bathymetric contours flare out at about 324 to 439 fathoms (1,944 to 2,634 feet), an area interpreted as the northeastern edge of the Hueneme Submarine Fan.  The fan's greatest depths were sounded up to 513 fathoms (3,078 feet).

The canyon is incised into the southwest edge of the Oxnard Plain, a subsiding series of alluvium interbedded with sandy beach and clayey lagoonal deposits (U.S.G.S, 1949; and Crowell, 1952). The headwall of the canyon is located just outside the Port Hueneme Harbor entrance, and with a buried canyon rim that is moderately resistant to wave-caused scour, when accompanied by moving sand.  The Hueneme Submarine Canyon is connected to the Hueneme Fan that has rough northwest trending, rectangular configuration with dimensions of 30 x 70 km (18.5 x 43.5 mi), and formed by turbidity currents, mapped by the U.S.G.S. (2009).  The Hueneme Canyon structure is important because this funnel-like conduit, when coupled with the longshore current, transports migrating sands and gravels south along the coast that are deflected by the northern jetty into the Hueneme Canyon-Fan system, and then the San Pedro Channel.