There is no such thing as water proof. If someone tells you something is water proof they are lying.
Items are water resistant and good products will state the conditions you must meet to keep it water resistant 99% of the time.
Silicon coating is a general insulator from dirt, scratches, water, and electrical contacts. It doesn't take much to compromise its protective properties, and if its not applied properly it will bead and leave some area's completely unprotected.
we use wax for underwater connector because it can be removed. But if you have temp extremes then it wouldn't work. The problem isn't what you can use for a coating. The problem is finding a coating that is possible to remove if you need to.
Some parts are cheap enough that removing the coating is not going to be a problem but removing the connection can be. So plan ahead and leave enough wire to cut a board free and still have enough wire to terminate it.
groundfungus:
Google 'conformal coating' for info on coatings for harsh environments.
Waterproofing is too general a term to respond to. Are you going to immerse the project in water? Is the project going to be so cold water will condense on surfaces? Is the project going to be in a hot and humid atmosphere?
Does your project have any connectors that will be connected or removed after conformal coating? Will the project have any mechanical switches or a piezo sound generator? These can't be conformal coated. An uncoated connector will be effected by moisture if water is allowed to condense on it's metal surfaces.
Will any component dissipate enough heat to effect the conformal coating. The coating will be a temperature insulator, no matter what you use.
Circuit board vias will allow moisture to penetrate if only one side of a circuit board is coated.
Conformal coating will have to be melted and cleaned off any component that needs to be replaced.
If the board has any socketed ICs, they cannot be conformal coated.
Probably there are more things to consider, but that is enough for now.