A whole house dehumidifier can be freestanding, piped into your ductwork, or you can add Tee's and tie it into the HVAC system so It serves your whole house and the basement. If humidity is really only an issue in the basement, you wouldn't need to tie it into your HVAC system. You have the option of using your dehumidifier only when the HVAC system is on depending how you wire it.
You don't want to rely on a dehumidifier if water is pouring in your basement. If there is crawl spaces with open sand you can create a vapor barrier with thick plastic , and like others said Dry-lok is a great product. if your foundation is cracked you may want to dig the exterior out and seal the crack from both sides
If you rely on a dehumidifier to get rid of 2" of standing water, the energy bill will be phenomenal. The 1850 model or 100 now (100 pint per day) will do it, but it will really hurt your wallet
as for mold, if you had standing water down there, I'd sterilize everything, have baking soda around and change monthly, put the grow tent up on a few pallets just in case. Anything else down there that might get moldy if water to come into the basement put those up on pallets too
It's good you're going to fix grade and gutters this summer that will be a big help. Remember your plants are in a basement so you will need to do a lot of extra work to prevent mold and mildew growth