Starting batteries are for starting only, not intended/designed for any heavy loads such as pumps. Yes, there can be a problem with using a starting battery for deep cycle applications while charging if that pump wants more energy than the charger can provide. Its probably not a good idea to use your battery charger as an AC/DC transformer for continuous, high demand applications. There are some chargers that are designed with heavy-duty components inside and can be used that way. But even with those chargers the DC demand (load) should not exceed the output of the charger or you risk supplementing the DC demand with energy from your starting battery taking the battery down.<br /><br />If you take a starting battery down deep and recharge it, your battery is preparing for its death. Do it a second time and your starting battery is almost a living shell. Three times and it is gone. I say gone but it may still start your engine if your engine is maintained, it just doesnt have any worthwhile capacity left and should be replaced.<br /><br />You mention you have a separate battery for the trolling motor. Its probably a deep cycle battery. Thats the kind of battery you need for running continuous running of that bait-well pump.
