Repoint the joints between the stones if you have an older stone foundation in your bulkhead. Repointing involves going over all of the mortar joints between the stones with a coat of fresh mortar, paying particular attention to any gaps or cracks that you see.
Repair damage and cracks in wooden bulkhead doors. Caulk between planks to prevent water seepage through the door itself. Replace rotted areas of the door by cutting these out and replacing them with new wood or, for small areas, filling them with auto body filler or an epoxy mix.
Replace any rubber or foam gaskets that are present on metal, plastic or wooden doors. Even a small gap in a door gasket can introduce a lot of water into your bulkhead, particularly if it's in the path of a flow of water.
Rearrange ground grading or gutters that may be directing excess water in the direction of your bulkhead. Grading the ground away from the bulkhead and putting gutters on any eaves that are above the bulkhead will greatly decrease the amount of water that is trying to get into the bulkhead.