During the takeoff run, at 85 kts, the acft hit a bump & the plt stated his forward vision was obstructed by water on the windshield. He instinctively pulled back on the controls & become airborne. He lost sight of the right side set of rwy lights & was reportedly flying 'blind.' The acft drifted left into trees & came to rest in shallow water in a backwater area 150 ft north of the departure end of rwy 10. Many of the rwy lights were either not operating or were obstructed. No lights in the last 1000 ft of the rwy were both operating & unobstructed. The NOAA arpt/facility director contains a remark for the arpt 'Runway subject to flooding after very heavy rains.' This remark does not appear in the Jeppesen 'Airport Directory' that the plt was using. After the accident the plt stated he walked through the eastern end of the rwy & found himself 'up to his ankles' in about 3 inches of water.