I assume this is a Docked boat? Seadoo states that their boats should not be left in the water.
Regardles, you have LOTS of work in front of you. I have to think it would be impossible for there NOT to be water in the oil. Once you drain the boat, check the oil BEFORE you try to start it. If there is water in the crankcase, you will need to change the oil and the filter.. The filter is a MUST do as the water gets trapped and the filter will collapse and the engine will not get oil. Once the oil and filter are changed, pull the plugs and crank the engine. Do NOT stand over the plug holes or put your fingers over them. Very dangerous as the force can easily tear your skin and inject your blood stream with all kinds of bad stuff. You should ground the plug wires and FLOOR the boat when cranking. By flooring the throttle this is suppose to disable the spark. Once you THINK you have all the water out from the cylinders, check the oil again,,, If it is mostly oil, then put the plugs in and see if you can get it to start. You will likely need need plugs as you go. If it does start, let it run for maybe a minute. Re-check the oil. I am certain it will be mixed with water. If so, change it and the filter again. It is common to take as many as four oil changes to get the water out. About on the third change it should be mostly oil. If so, you MUST take it for at least a 30 minute ride to get the entire block up to temerature. This will do two thngs. The temp will get the residual water to evaporate and the higher RPMs will get oil everywhere it needs to be in order to flush the engine of the water that will still be inside of it. You will likely need to do another oil change after the 30 minute run...