Hi Harnam,
A good challenge to explore!
Perhaps take a look at the EEPromWriteAnything Arduino example which shows a technique to read and write values longer than a byte (like the 'unsigned long' values stored in the water flow sketch). The example there should give you some ideas about how to go about it:
http://playground.arduino.cc/Code/EEPROMWriteAnything
Bear in mind the EEPROM only supports a finite number of writes (100,000 is all that's guaranteed) before it wears out, so you'll need to make a decision about how often to update the value - for instance if you save a different value every second then you'll hit the write limit in just over a day, if you save every minute then a bit over two months, every hour then close to twelve years, etc.
One thing you can do is make sure you don't write a new value if it hasn't changed from the old value (assuming the water flow doesn't change much.)
Other forum peeps might have some other inventive ideas on how to save the values.
- Angus