Now all that is left is for you is to put your connected electronics (5V power supply, the Arduino Pro mini, and the relay) in the junction box and stick them using a hot-melt glue gun.
You may also use the hot-melt glue to waterproof any other parts that may need waterproofing:
After placing the Arduino, relay, and the 5V power supply safely in the junction box, connect your drip irrigation system to the submersible pump and submerge the connected pump in your water reservoir. Place your drip irrigation system to directly water the roots of your plants and finally switch on the pump power supply.