I'm trying to estimate how long my batteries should last on a fishing outing.  I don't know much about boats, so I'm sorry if this is a dumb question.

In addition to my cranking battery, I have three 100 amp hour deep cycle batteries.  According to Minn Kota, my trolling motor's max amp draw is 46.  If I run my trolling motor at max power, is it correct for me to expect my batteries to last (3 batteries)*(100 amp hours per battery)/(46 amps) = 6.5 hours?  

I'm not getting anywhere near six hours of battery life when I run my trolling motor at 25-50%, so I think there's something wrong.

How are you using the batteries?  Are they connected in series and you are running a 36 volt motor, if so your math is flawed.  Even though they are 100Ah, if connected in series the triple the voltage but still at only 100Ah.  If they are connected in parallel, then they would triple the capacity to 300Ah but still only have 12 volts.

Also, there's a little more involved even if you are running them in parallel  Theoretically you would be right if it weren't for way they rate the batteries and the way you use them.  Your battery is rated on a 20 hour scale, meaning that they only use enough current to discharge the over a 20 hour period, that's about 5 amps.   As the current draw increases, due to the internal resistance of the battery, the efficiency of the battery decreases.  In real life and actual use if you were to be pulling 45 amps off three batteries in parallel, you would probably loose about 15 to 20% of the rated capacity so you would have to figure about 20% less run time.  However, if you are running them in series and pulling 45 amps, you would be loosing about 35 to 40% capacity so you would have to figure that much less run time.

Now if you are not running them at the full 45 amp draw, then your efficiency is going to be lower than the 20 hour rating, but higher than the full load rating.  

A better indicator of what your run time would be is the reserve capacity rating.   That is how many minutes the battery will run with a 25 amp draw (some batteries use a different amp draw usually it will be between 20 and 25 amps, you have to check their specification sheet).  Typically, 15 to 25 amps is more common to what your will draw when fishing and casting so if the battery has a RC rating of 180, that means you should get close to 180 minutes of just easing around and casting. 

Depending on the type battery, if fairly easy to check them yourself with a voltmeter and hydrometer if you think one is bad.

Thanks for the response, Way2slow.  Much appreciated.  

The batteries are connected in parallel. The 20% less run time figure helps a lot.  

I'll invest in the voltmeter and hydrometer.