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Finally, a topic that I feel qualified to answer! In "real life" I'm an electrical engineer...

The term for completely discharging and recharging a battery is called "deep cycling".

Lead Acid type batteries do not like deep cycling. Standard car batteries can be damaged quite a bit by deep cycling. Do it too many times and your battery will stop taking a charge. Leaving your lights on is really bad for most car batteries. Some lead acid batteries are labled as "Deep Cycle", as in "Deep Cycle Marine". These batteries are more difficult to kill by deep cycling, but I wouldn't tempt fate if possible.

NiCD batteries, and to a lesser extent NMHi, prefer to be deep cycled. They have a "memory effect" (which is a misleading name for the problem). Essentially, if you don't deep discharge them then they will tend to loose their ability to keep a charge. _BUT_, and this is a big _BUT_, deep discharging them incorrectly can be worse than not doing it at all. Let's say that you have a flashlight with four NiCD's in it. You "could" deep discharge it by leaving the light on for a day, but this would be bad... What happens is that each battery will have a slightly different charge in it, so as the flashlight burns down one battery will completely discharge before the others. If you work out your electrical theory stuff you can figure that the dead battery will essentially be charged IN REVERSE POLARITY by the remaining batteries. Charging in reverse polarity is a quick way to kill a NiCD or NMHi battery.

For most people, the best way to deep discharge NiCD or NMHi batteries is to "mostly deep discharge" them. That is, run the batteries down but don't let them go all the way down. Most electronic equiptment (cameras, MP3 players, PDA's, GPS's) are not capable of completely draining a battery. But things like motors and lights are able to do that. So for these devices, turn them off when the light is no longer useable or the motor no longer turns with enough power to be useful.

Lithium Ion batteries seem to be the most immune from charge/discharge related issues, but I still wouldn't deep discharge them-- only a mostly deep discharge. Also, most Li Ion equiptment has more sophisticated charge/discharge circuits in them to prevent these issues.

So, in the case of your boat... If your battery is a Lead Acid, for the trolling motor or whatever, then you should keep it topped off.
 

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Right. Don't leave any lead acid battery uncharged if you can help it.

But, Dan, you email implies that your charger has a "deep cycle" setting. This could mean many things, so the best thing in that case is to consult the manual. There are NiCD/NMHi chargers that will first discharge the battery then charge it. This is appropriate for those batteries, but not for Lead Acid batteries.
 
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