Find another mechanic
Either have him show you exactly how it's happening or find another mechanic. The fuel system is closed loop and sealed. If you had any way for water to get into the fuel pump you would also see fuel leaking from that spot. The pressure from the fuel flowing would cause it to leak. Water and or gunk getting into the fuel pump is most likely coming from the fuel tank. You were told it was cleaned and it most likely was but depending on the degree of contamination it may not have been cleaned well enough. It's a pain but the best thing to do is to empty the fuel tank (disgard the fuel)and clean it like you were going to perform surgery in there. There should be an access port on top of the tank. Once the tank is spotless, then change out the primary and secondary filters, add fresh diesel fuel treated with a biocide and fire her up. You may have some residual gunk in the fuel lines but fresh filters should catch that. Worse case you may need to change filters a couple of more times. The fuel pump should be OK. If it appears like it's not pumping strongly enough (can't get full power) check the inlet side of the pump. Remove the fitting and there will likely be a small filter behind it. Most pump manufacturers install one on the intake side. The filter, if dirty, will either have to be cleaned or replaced. Sorry to say once diesel fuel systems are contaminated they are a royal pain to clean but that's about your only choice. Good luck.