Question about irrigation system valve box

Hi, I noticed that after a good rain storm, the valve box of my irrigation system is flooded. I would expect this since it sits at a low point in my backyard. My irrigation company told me not to worry about this since all the components are waterproof. I have my doubts that these components and wiring were designed to be in standing water.
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If it was done well all the conectors are silicone filled and should be fine as the water pressure of less than a foot of water is minimal. Time will tell.
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