The Goleta Slough is an area where fresh water and ocean water meet, but a sand berm is blocking the natural flow.
The water is flooding the area between the Santa Barbara Airport and Goleta Beach.
A pipeline was put in to siphon the water off, but it isn't working fast enough.
Mosquito management experts say they caught 25,000 mosquitoes in traps during one night, usually they only catch 200.
And the mosquitoes are the kind that can carry the West Nile virus.
The area is also attracting large birds though could cause airplane bird strikes.
Airport planners wanted to bulldoze the sand and silt that has built up since March, but that could threaten endangered steelhead trout.
Airport planners instend to ask the California Coastal Commission and the Army Corps of Engineers for permission.
The flooding has also stalled work on a fish ladder in the San Jose Creek.