There are 2 ways: 1) The seller waterproofs the basement before closing, and the repairs are verified and inspected by the appraiser.
2) You can get an FHA 203 (k) loan which allows for the purchase and repairs as one loan. So if you are buying the house for $150,000 and the waterproofing requires $15,000 in repairs, then you would need your 3.5% down of the $165,000 total, and the $15,000 is set aside for the waterproofing.
In these cases, the purchase price is often renegotiated to take the repairs into account.
Contact me with any questions.