On September 28, 2003, approximately 1400 Pacific daylight time, a homebuilt Thompson Avid Flyer, N6611, registered to and being operated/flown by a private pilot sustained substantial damage during a ditching along the shoreline of San Juan Island, three nautical miles east of Roche Harbor, Washington. The pilot and his son were uninjured. Visual meteorological conditions existed and no flight plan had been filed. The flight, which was personal, was operated under 14 CFR 91, and had departed the Roche Harbor private airstrip approximately 10 minutes earlier and was destined for Snohomish, Washington. The pilot reported that he departed Snohomish earlier in the day with a full load (22 gallons) of fuel aboard. The straight-line distance from Snohomish to Roche Harbor is approximately 50 nautical miles and the pilot reported that the aircraft's engine consumed about 5 gallons per hour (refer to Attachment D-I). Following the landing at Roche Harbor, the aircraft was parked on a slope with the right wing lower than the left and no gas was added. The pilot reported that he did not see any significant evidence of fuel leakage when he returned to the aircraft approximately 2 hours later. Prior to departure from Roche Harbor he noted a significant imbalance in the fuel between the two wings with the right wing being full and the left wing indicating the "presence of gas." After takeoff the pilot noted that the fuel was not equalizing between the two tanks and decided to land at Friday Harbor. Shortly thereafter, at 1500 feet above sea level, the Bombardier-Rotax two-stroke 65 horsepower engine quit. The pilot executed various procedures including activating the fuel boost pump, checking the fuel flow and activating the starter all without success; and then ditched the aircraft off Mineral Point. A passing boater rescued the two occupants, tied a rope to the aircraft and towed it to the nearby shoreline where it was pulled up on land. The pilot reported that upon beaching the aircraft the right wing was observed to have substantial fuel in its tank. This fuel was removed from the tank and estimated to be about 15 gallons including some water. The fuel selector on the aircraft was reported by the pilot to be an "ON-OFF" selector with both fuel tanks feeding a common, single header. An inspector assigned to the Federal Aviation Administration's Renton Flight Standards District Office examined the aircraft following its recovery. He found no evidence of any water related pre-impact mechanical malfunction within the engine. Additionally, upon examination of the carburetor he reported finding both carburetor bowls filled with auto gas with one or two drops of water in each. The inspector found the fuel valve to the right wing tank to be open with no apparent obstructions within the line (refer to attachment EM-I).