Assuming you dont have a cracked lower unit housing......water would be getting in via one or more of the seals or washers.....every shaft, rod, bolt or screw that goes INSIDE the housing will have some type of seal.
Start by replacing the lower unit oil drain and vent screw washers and retry.....
Check the drain and fill plug seals first. If they are damaged, they can leak water into the case and are a cheap and easy replacement item. When you reseal the lower unit, the following seals get replaced. Any of them can leak water into the lower unit: Propshaft seals. Carrier oring. Carrier bolt seals. Driveshaft seal. Shift shaft oring. Shift shaft cover gasket. Driveshaft housing oring. Follow boobie's suggestion and have the lower pressure and vacuum checked at a marine dealership.