water on an alternator will definately impair things. think of it this way, its job is to make electricity, electricity+water=bad news.
Anyways, put a multimeter across the battery teminals. under load and at idle it should read 13.8-14.8 volts. If this is not the case have the battery tested to see if it is the problem.
below is from
http://www.uuhome.de/william.darden/carfaq5.htm
When the charging system fails, usually a "battery" or "alternator" warning indicator or light will come on or the voltage (or amp) gauge will not register "good". If you increase the engine speed and the alternator light becomes brighter, then the battery needs to be fully recharged and tested. If the light becomes dimmer then the problem is most likely in the charging system. The indicator (also known as an "idiot") light is a direct comparison between the voltage output of charging system and the voltage output of the battery. The next test requires use of a known-to-be-good, fully charged battery. Temporarily replace the old battery with this battery and run the engine at 2500 RPM or more for two minutes. Depending on the load and ambient temperature, the voltage should increase to between 13.0 and 15.1 volts during this period. Most vehicles with good charging systems will measure between 13.8 and 14.8 volts on a warm day, depending on the battery type that the charging system was designed for.
If a battery terminal's voltage is below 13.0 volts with the engine running and the battery tests good after being recharged or if you are still having problems keeping the car battery charged, then have the charging system's output voltage and load tested. Also, have the car's parasitic load, the electrical load with the ignition key turned off, tested. (Please see Section 10.) A slipping alternator belt or open diode will significantly reduce the alternator's output capacity. If the output voltage is above 15.1 volts with the ambient temperature above freezing, if the battery's electrolyte level is frequently low, "boiling", or if there is a "rotten egg" odor present around the battery, then the battery is being overcharged and the vehicle's charging system should be tested.
From Another Site
If you need to check the alternator, all you need is a voltmeter. Make sure you have a good battery. Start the engine and engage the clutch handle. Set the voltmeter on DC voltage. Take the red lead of the voltmeter and put it on the large red wire at the alternator. Put the black lead on the alternator housing. With the engine at high idle, you should have a reading of 14.2 - 14.6 volts. Take the voltmeter to the battery and place the red lead on positive and the black on negative. You should be reading 14.2 - 14.6 volts. If not, you have a wiring problem to the battery. If you do have 14.2 - 14.6 volts and you still have slow function problems, test the battery.