A fuel filter assembly (200) employs a base (212) having a canister configuration for receiving and mounting a disposable filter element cartridge (214). The cartridge (214) includes a dual stage filter system wherein fuel flows axially to a primary filter element (274) for removing particulate matter and coalescing water droplets and axially to a secondary filter stage (292) which functions as a water barrier. The filtered fuel flows axially and through an outlet passage (249) in the base. Water may be collected in a sump (242). The cartridge is retained on the base by a collar (263) which engages against a roll seam structure (281) of the cartridge.