My main breaker kicked yesterday and I had no power in my house when checking the breakers I found that every time I turned my water heater breaker on it would kick the main breaker to the whole house.

You have a short in a wire leading to the HW heater or perhaps a grounded heating element. If you are comfortable analyzing the 240VAC circuits, turn off the HW breaker, disconnect the wires at the HW heater and AFTER making sure the input power lines are not touching anything, turn the HW breaker back on. If the main breaker trips, the problem is in the wire, if it doesn't, the problem is in the HW heater, probably a grounded element.