Waterproofing Arduino
You can just solder everything you need to the Arduino (I would recommend using an Arduino Mini since it has no communication port) and coat it with Silicon Conformal Coating. It creates a silicon layer on top of the PCB that would not let any moisture through. Or you can just put it in a case and cover it with epoxy, that will be even more protection, but there will be no more access to the board unless you foresee it.