Water consumption in kWh???
The frequency for transmitting your data will depend on the pulse frequency and how up-to-date your information has to be. It doesn't make much sense to send an update every hour if you get on average only 1 pulse per hour. In that case once every day or so will do. You could send each time you've counted, say, 10 pulses, but then you won't send anything if you're away for a week, and the receiver may want more frequent updates. A better alternative is therefore to send at fixed time intervals, like every day at noon and at midnight.
For the reliability of the data transfer you have a number of options. The RFM12B radio modules are transceivers, so you can let the receiver send an acknowledge. Not exactly complicated, but it can even more simple, with one-way communication. The word is redundancy. Lots of it. That's often a bad word, but here our data volume is so low that some redundancy won't do any harm; it would hardly be worthwhile to switch on the transmitter to send two bytes, would it?
Now sending 5 copies of the same data in the same transmission is not a good idea. The redundancy is no use if the complete transmission gets jammed. Here's what you do: the N-th transmission sends the following:
• the counter value N (1 byte will do)
• the N-4 th data
• the N-3 th data
• the N-2 nd data
• the N-1 st data
• the new data
• Hamming ECC
I would send cumulative data, for instance 16-bit numbers. If you have a pulse per 0.1 m\$^3\$ of water you'll have an overflow after a couple of years, but the receiver should have no problem with that.
That will give you a payload of still only a few dozen bytes, but ensure you that all data gets received even when 4 consecutive transmissions are lost. If it makes you sleep better you can still combine this with an acknowledge and a re-transmit if needed.
The microcontroller will have almost nothing to do: keep a timer to keep the time until the next transmission, and count incoming pulses. You can run it off a cheap 32.768 kHz crystal. Even without using the low-power modes an MSP430F1101A will only use a negligible couple of µA; your power supply will consume a multiple of that. Only switch on the transmitter twice a day to send your data.
Your microcontroller will have to run continuously for months, and then you have to take power-cuts into account. Where I live they are rare; the last one dates from 3 years back and lasted 15 minutes, but I've been told they're more frequent in rural areas in the US where there are many overhead powerlines. Anyway, you want a battery backup to keep the controller running during a power outage. A CR2032 cell and an MSP430 is enough for eternity. OR the battery's output with the mains power supply (3.3V) with a couple of diodes. Postpone transmissions when running on battery power.
There's no need to store the counters in EEPROM, just keep them in RAM.