How to water-protect my Arduino?
In a nutshell, you want to treat the Arduino and all other electronic components as you would treat a line voltage electrical system. You want to have a weather-resistant case for the Arduino with as few access ports as possible, and you may want to go so far as to plug those access ports with silicone once you have the required wires in place. The easiest way to protect it from the actual watering system is simply to have the electronics at a higher elevation than the water source, while observing all the previous precautions I mentioned.