Several things...

If you want to monitor more than one meter/device, consider using a multiplexer and polling. A multiplexer is a circuit that switches between inputs or outputs based on the status of an address or 'SELECT" pin. Here's a link to a very simple one:

http://www.toshiba.com/taec/components2/Datasheet_Sync//168/7380.pdf

They come in lots of flavors. You could then use your Arduino to select which meter you want to listen to. One way to do this would be to sample the rate (switching to a new meter and counting ticks for a period of time to measure flow rate, then switching to next meter). You'd lose absolute volume information between samples, but you could estimate it from the sample info. Alternatively, you could load hardware between the Arduino and your meters so that the meter ticks acted as clocks on accumulators (counters), which the polling software then reads & clears/resets.

Regarding detecting problems...

It seems you want to detect changes over time as well as absolute values over time. For changes, capturing differences is what you want. So if today's value is 1000 gallons but yesterday was 400 gallons, that's a change of 600 gallons. If you measure your daily fluctuations for a bit and find that the average fluctuation (standard deviation) is, say, 200 gallons; then a change of 600 gallons is very unusual (probably happening less than 2% of the time). One the other hand, if you accumulate values (adding yesterday to todays for a period of, say, 7 days), then you can compare to your expected totals over that time and again decide whether to sound an alarm.

Locating problems...

If you have 200 places where you might have problems, and you want to speed up locating the problem, you can decide how many places are a reasonable number ro check manually as compared to the cost of having the meters. So, for example, if it's expected that it will take 15 minutes per spot to check, and your person checking is paid $10/hr, that's $2.50/spot. If you estimate that leak problems will happen 6 times / year, then it's $15 per spot per year. If you estimate that your meters will last 5 years, then it's $75 per spot / 5 years to check manually as compared to the meter cost. If the meters cost less than that, you'd be justified in having a meter per spot; if not then divide into the meter cost to determine how many to use.
That said, you only need 2 meters to split the area in half, 4 to split it into quarters, etc. Using a binary search, you can sample branches of branches to locate which area has the problem.

Okay, so that's a lot and maybe not all that clear, but I hope it helps. Please feel free to ask clarifying questions.