The 1700 hour instrument rated pilot was familiar with the route of flight between Hayward (HWD) and San Carlos (SQL) having reportedly flown the route to work over 100 times. The pilot's SQL destination did not have a published instrument approach. So, the pilot planned to execute an IFR approach to HWD and then initially fly under SVFR toward SQL. Approaching SQL the pilot planned to request a SVFR clearance into its control zone. While flying enroute the pilot would be over open water in uncontrolled airspace where only one mile of flight visibility would be required. After executing the instrument approach to HWD the pilot received, as planned, the requested clearance out of its control zone. After receiving a SVFR clearance into SQL's control zone the pilot failed to maintain altitude and he descended into the San Francisco Bay. At the time the pilot was in HWD's airspace, its weather was, in part: 200 foot overcast ceiling and one mile visibility in fog.