On February 6, 2008, at approximately 1955 eastern standard time (EST), the pilot of N140FT, a Piper PA-28-161, departed on runway 6 at St. Augustine (SGJ) Airport, St. Augustine, FL, and ran off the end of the runway into the marshy waters of the Intracoastal Waterway. There were no injuries to the sole occupant of the airplane and there was only minor damage to the airplane. The pilot was operating the airplane under the provisions of 14 Code of Federal Regulations Part 91, and the pilot had filed a visual flight rules flight plan. At the time of the incident, the flight was departing from SGJ destined for Deland, Florida. The incident occurred during night visual meteorological conditions. At the time of the incident, there were two controllers scheduled to work; however, one controller who was scheduled for duty until 2030 EST left the facility at approximately 1815 EST. At 1944:40, the pilot of N140FT contacted SGJ air traffic control tower (ATCT) about 10 miles south of the airport with automatic terminal information service (ATIS) information "Juliet" and requested a full stop landing. About 15 seconds later, the controller instructed the pilot to report the inlet inbound, which was about 5 miles south of the airport, for a straight in approach for runway 31. The pilot acknowledged the clearance. At 1948:38, the controller cleared the pilot to land on runway 31. About 4 seconds later, the pilot acknowledged the landing clearance. At 1951:21, after N140FT had completed his landing roll, the controller asked the pilot his intentions. The pilot said, "Ah, that's foxtrot tango. Would like, uh, taxi back, and takeoff to Deland for foxtrot tango." At 1951:31, the controller instructed the pilot, "Make the next left turn. You can taxi to runway 31. Hold short of runway 31 at [taxiway] bravo four. Advise when ready." About 7 seconds later, the pilot said, "Taxi back, next taxi back to [runway 31] three one and hold short for one four zero foxtrot tango." At 1952:51, the Airport 4 vehicle operator radioed the tower and requested, "And it's Airport 4, I'm holding short of runway 13 at [taxiway] alpha 2. Request to take a run down runway 13." The controller instructed Airport 4 to proceed onto runway 13. At 1954:02, the controller announced the new ATIS code over ground control frequency. At 1954:39, the Airport 4 vehicle operator advised the tower that he was clear of runway 13 at taxiway B4. The controller acknowledged. At 1954:43, the controller phoned the Lockheed Martin flight service station (FSS) controller to update SGJ weather information. About 45 seconds later, the phone call was terminated by both controllers stating their operating initials. At 1955:20, the pilot contacted the controller and requested progressive taxi instructions. At 1955:36, the controller told the pilot, "You're fine where you're at. Are you ready to go?" About 4 seconds later, the pilot said, "Yes, ma'am one four zero foxtrot tango is ready to go." At 1955:43, the controller instructed "Zero foxtrot tango, runway 31 at runway six intersection, cleared for takeoff left turn southbound." At 1955:48, the pilot said, "Cleared for takeoff. Left turn southbound, one four zero foxtrot tango." The pilot advised investigators after the incident that he understood that to mean he was on runway 31 and cleared for takeoff. Thus he completed the pre-takeoff checklist and began the ground roll. He further stated that he noticed he was on the wrong runway and tried to stop, but it was too late to stop and the momentum carried him into the marsh. At approximately 1956, the controller stated during her interview that she processed the significant meteorological weather data that had printed out on the flight data input/output computer. The controller said, "She then looked to the northwest and saw lights on the horizon she believed were from N140FT." At approximately 2013, while the controller was inputting the tower traffic count on the scheduling computer, the motion detector alerted to the possibility of someone being at the base of the tower. The tower doorbell rang, she answered the call, and a male voice said, "I went off the runway into the water." The controller asked if he was okay. He stated he was "a little wet." After a brief conversation with the person via the intercom, the controller determined the person was the pilot of N140FT. She asked if he was a student solo and if there was anyone else in the airplane. The pilot replied, "No." The controller instructed the pilot to remain at the base of the tower and she immediately initiated the facility accident/incident notification procedures. In her interview, the controller stated she decided not to notify airport rescue fire fighting (ARFF) because the pilot had stated to her that he was okay and based on her previous experience as a dispatcher at an emergency dispatch communication center, she believed it would have been an unnecessary expenditure of resources. The airport remained open for the duration of the event. At 2024:35, the Airport 4 vehicle operator informed the controller that the airplane was right off the approach end of runway 24. PERSONNEL INFORMATION For the past 5 years, the SGJ federal contract tower (FCT) controller had been appropriately certified and qualified to perform her assigned duties. She received her initial control tower operator's certificate on July 5, 2003, at Craig Municipal Airport, Jacksonville, FL. The controller was certified to take limited aviation weather reporting service (LAWRS) observations. METEOROLOGICAL INFORMATION The special weather information requested for the aircraft incident: SGJ SPECI 0215 UTC (2115 EST); wind 240 degrees at 8 gusting 14 knots, visibility 10 statute miles, sky clear, temperature 23 degrees Celsius, dew point 12 degrees Celsius, altimeter 29.97. WRECKAGE AND IMPACT INFORMATION There was minor damage reported to the aircraft. ADDITIONAL INFORMATION Airport Information: SGJ had three runways - 2/20, 6/24, and 13/31- as well as three sea-lanes. Runway 13/31 and runway 6/24 intersected, with 560 feet remaining for a pilot to depart on runway 6. Runway 6/24 was asphalt and reported to be in good condition. The airport field elevation was 10 feet mean sea level (MSL). SGJ FCT Information: SGJ FCT was owned and operated by the Robinson Aviation Inc. (RVA). It had been a part-time facility since October 3, 2002. The facility operating hours were 0700 to 2100 EST/0700 to 2200 EDT; at the time of the incident the tower was open. On February 6, 2008, SGJ FCT was authorized five certified professional controllers (CPC) and one air traffic manager (ATM). The facility was authorized to reduce to one controller daily from 2030 to 2100 EST as traffic volume dictated.