Motor not running right when submerged

I have a 90hp Yamaha. It's been while since running it but it starts up fine out of the water with the head phones on. When I put it in the lake the motor starts up but doesn't want to idle right or go into drive. Could the gas be bad? Any ideas on what is wrong with it.

How would bad gas be the problem when the run/doesn't-run difference is whether the lower unit is submerged or not? The motor is running on the same fuel in both cases. Have you thought about this?

Submerging the lower unit introduces a certain amount of exhaust back-pressure. If the engine isn't set at a proper idle RPM (or the idle RPM has decreased due to an engine issue) then said engine won't be inclined to idle very well. An engine not idling well typically struggles when the prop load is introduced at the low RPM. You may have an idle setting that crept on its own, or a lower idle as a symptom of some other engine issue. Less than ideal spark from marginal plugs could even be a culprit, for instance. It's unlikely your gas. Running from a borrowed portable tank would prove this quickly, but I think that's a waste - you likely have some other minor issue. Check the idle RPM, then look for why it's too low.

Sometimes with bad gas they will run on the muffs but die once you try to run in the water. You likely hAve water in your fuel, take fuel line off and put some in clear jar to check. It will also smell bad if it's to old. Really if by some time you mean 3 months or more and your tank wasnt empty or full to top I would dump that gas, it's not good and even if it was treated that doesn't keep water from getting in the tank. I would make no adjustments without knowing I had good fuel as adjustments with bad gas won't be right with good gas. Is it carbed or injected? In a carbed motor it will get water in the bowls and get enough gas to start but when you try to load it it starves and dies.

Also fuel pumps carbs ect can cause this prob.

You really need to connect to a remote fuel tank with good gas and try it. Yamahas are sensitive to old gas.

As are their carbs. Everytime my Yammy 50 has done this, it just meant the carburetors needed attention. Once you get them right, do yourself a favor and only run non-ethanol gas. Used to have to have my carbs serviced every year. Since I started running non-ethanol exclusively, haven't had to have my carbs worked on in 5 years.

Keep in mind, if you run your boat a lot, non-ethanol gas shouldn't be an issue. But if you are like me, and only get your boat out every few months, then non-ethanol is worth every penny and the distance I have to drive to get it.

I have a 50hp Yammy and agree. FYI Murphy Oil in front of Walmart in Brownwood, Texas has Non-ethanol. Was $2.32 a gallon yesterday. I assume Walmarts will continue to add this option.

My neighbor has a 70 Yamaha 2-stroke and he uses it 6 months and then stores it for 6 months. He uses gas conditioner, and every year he has problems related to carbs and bad ethanol gas. His boat mechanic told him the conditioner will only protect your engine for three months. I told him he needs to drain the tank and run it dry before he stores it, and he will save himself a lot of grief.
I have a 1961 Johnson 5.5 Twin on my flats skiff and I've been running ethanol gas in it for a year, and I haven't had any troubles, but I don't let it sit very long between outings. I was told that the cork float would decompose, because of the alcohol, but it seems to be fine. Maybe corks were better 55 years ago!
Island Jim