The pad was fixed prior to the second test launch with the addition of a water deluge system.
The clean water act issue involved a dispute between Texas and the EPA about which kind of Texas permit SpaceX needed for a potable (drinkable) water deluge at the pad. Texas regulators told SpaceX what they needed to do for permitting, SpaceX did it, and then the EPA came back and made them file different paperwork and pay a fine. My understanding is that the EPA did not require any changes to the deluge system, just different paperwork.
SpaceX concluded that paying the fine was faster than fighting the EPA.
The clean water act issue involved a dispute between Texas and the EPA about which kind of Texas permit SpaceX needed for a potable (drinkable) water deluge at the pad. Texas regulators told SpaceX what they needed to do for permitting, SpaceX did it, and then the EPA came back and made them file different paperwork and pay a fine. My understanding is that the EPA did not require any changes to the deluge system, just different paperwork.
SpaceX concluded that paying the fine was faster than fighting the EPA.
SpaceX's version of events:
https://twitter.com/SpaceX/status/1823080774012481862