how to saving flow water meter reading into EEPROM

Other Hardware Sensors
6

That code won't even compile. The reason why would be more obvious if you had done an Auto Format as I requested.

I don't know how you know it's back to 0, since you never output the value read from the EEPROM in the code.

I suspect this code doesn't do what you think it does:

void water_daily(){
 if (totalMilliLitres > 0)
 {
  eeprom_daily = totalMilliLitres /1000;
 }
  else
 eeprom_daily != totalMilliLitres /1000;
 Serial.println ("water_daily");
 EEPROM.put(13,eeprom_daily);
 
}

Again, Auto Format makes things more clear:

void water_daily() {
  if (totalMilliLitres > 0)
  {
    eeprom_daily = totalMilliLitres / 1000;
  }
  else
    eeprom_daily != totalMilliLitres / 1000;
  Serial.println ("water_daily");
  EEPROM.put(13, eeprom_daily);

}

This line:

   eeprom_daily != totalMilliLitres / 1000;

does nothing.