Mike,
First of all we need to know how much water power you have to harvest. How much water? How far does it fall? Can you legally alter the streambed? Is it a constant flow? Details are our forte here. :-)
One needs to choose the generator/alternator based on some of the above info. A big overshot wheel can maintain a pretty good state of steady RPM if not overloaded. That's the deal, making a steady state (rpm wise) water powered source. I'd give a bunch for just a small spring to tap some power.
Diversion loads can be eliminated from an overshot. When the batteries get all they need just have a simple water cutoff to the wheel. (I'd want that shutoff feature anyway).
With nearly any type of water powered rotational machine generating your electrical power you'll need a gearing ratio of a given rate of some kind. Belts don't mind running with a little water on them. A countershaft to the protected gen/alt and bingo. (I assume you are not talking abut building an enclosed turbine). Either the AC gen head or an induction motor will have to spin pretty fast. While you can harvest a great deal of torque from a simple water wheel the chances of getting high rpm is another matter. Some type of gearing would be needed even for a lower RPM PM alternator.
So give us the details and the users here will bend over backwards to help.