Re: 1988 Johnson 110 hp starts out of water but not in water.
(Engine Won't Start or Hard Starting In Water)
(Joe Reeves)
The Evinrude and Johnson engines, starting in 1973, have what is called Magneto Capacitance Discharge ignition, self contained, not dependent on battery voltage. The engine must turn over at least 300 rpms in order for the flywheel magnets rotating past the stator ignition generating coils to supply approximately 300v AC to the powerpack(s), which in turn is needed to supply power to the coils etc etc (spark).
In the water, exhaust back pressure is encountered due to the fact that the exhaust housing (housing between the powerhead and the lower unit) is filled with water. This would drag down the needed rpms, affecting ignition.
Normally the clue to this type problem is that the engine starts fine on a flushette (hose), but is very difficult to start when in the water.
Should this be the case, check the battery, clean and tighten all conections (use a wrench or pliers, not your fingers). Any cable that gets overly warm or hot indicates either a loose, or tight but dirty, or internally corroded cable. And of course check the starter itself.