How does pH affect covalent catalysis if it does?

If you are asking about covalent catalysis in terms of enzyme-catalyzed reactions, the pH of the solution can affect the ionization state of the amino acid side chain in the active site that is involved in the formation of a covalent bond with the substrate, or the ionization state of other active site side chains that are involved in the catalytic mechanism. Without knowing which specific enzyme you are concerned with, it is impossible to predict. But, if you look at a specific mechanism, you might see that an unprotonated histidine is required to abstract a proton from the substrate (or other residue) in order to form a covalent bond between an active site residue and the substrate. If the pH is lowered so that histidine is protonated, it will be unable to remove that proton, and the reaction will be inhibited.