You may have water in the pipe and or the carbs. I always drain them both.
Could also have water in the fuel tank if the quad was in deep.I take the spark plugs out and crank the engine a few seconds to purge the water in the cylinders or heads. Replace the spark plugs with new ones. Just make everything is dry. The use of lots of choke will usually let the engine catch, when it does keep the RPM slightly elevated until the engine is warmed up.
I let my quads run for 15+ minutes to mix the water and hot engine oil then drain the crankcase and oil filter again, do over until the engine oil show mo sign of water.
Good luck
Green 2007 750 Brute.14" SS 108 Wheels on 30" Mud Lites. VDI CDI, Dalton Clutch Kit. Full Muzzy PRO Exhaust system. Pen Lock, Hand + Thumb warmers, Over Fenders [flares] Per Fex Long travel kit. K + N air cleaner.