Why Doe's my Honda CR-V 1998 make a clunking noice wend drive over a pump?

Could be one of several things - remember your CR-V is now over 10 years old. I will try to list several possibilities - not necessarily in the order of priority - but you will have to have them checked out. Bad constant velocity joint(s) (CV joint). Broken motor mount or transmission mount. Loose exhaust pipe or muffler hitting the body. Bad or broken shock absorber(s) or strut(s). These are the first things that come to mind, and I'm not saying that your mechanic didn't NEED to do the original repair, but he definitely has to look further if you are still experiencing it.