Boat Shed Without Electricity - Solar Battery Charging?

your panels will come with a charge controller so you won't cook them
normally most charge at 6 to 8 amps

get the panel on amazon any RV type panels will be fine

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It's a 48V tolling motor. Do I need to isolate the batteries from each other while charging and have two solar chargers?

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You should be able to find 48V regulators/chargers for your solar panels.

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Any particular brand of solar charger to look at? I do not want to cook the batteries

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Most will cutoff charging if your voltage goes over a predetermined amount. That will be dictated by the battery type.

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What size solar charger?

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Kind of depends how often you use your boat/how fast you need a recharge. I saw someone suggested 6-8 Amps, that should be plenty if you plan on it being several days between uses.

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Any risk of damaging the on board (120V) chargers with a solar set up?

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That realy depends on your chargers but unlikely. If you want to be certain, you can either set up power diodes to prevent back flow or get a load sharing device that only isolates each source.