DLJ has some nice water meters at watermeters.com that feature a tick for every gallon that passes through them. I have used them before, great performance and good cost.
I second only using the ISR to increment the flow count and then going back to the main loop. Periodically, read and clear the accumulated flow ticks. In the past, I would have even steered you in the direction of the Dallas/Maxim line of 1-wire accumulators (great chips!) in order to monitor multiple water meters but alas Dallas/Maxim decided to discontinue them and not offer a replacement. So make do with the two hardware interrupt pins you have or use the PinChangeInt function to add more interrupts.
You should also consider using an RTC if you want to log the time accurately... I have had great luck with the DS3231 series. The Chronodot is available in a breadboard version, works great. Simply program the thing to output a square wave at 1Hz and you have a great timing system.