Does the contractor liable to repair the stagnant water areas on the hauling route?
Attempts to get more information from the question submitter were unsuccessful. As a result the best answer we can provide is and we have to mention the road is not government (real property) that was provided to the contractor.
1. If this is a construction contract (SABER or MATOC), possibly FAR 52.236-10(c) could apply if it is in your base contract. But it appears the underlying cause of the damage was the rain and other traffic (the tanks) and not through the fault of the contractor. It also appears the contractor at least made a good faith effort to repair it. I don't think the government would fare well if this turned into a dispute and went to ASBCA or COFC, or even arbitration for that matter.
2. If this is not a construction contract, the answer depends on what that "paragraph" mentioned actually says about maintaining the hauling route and what the performance requirements and/or quality standards are. Depending on that, any government rights or remedies would be tied to the inspection clause in the contract.