Taking antibiotics amoxil (amoxicillin). how long would it take to notice side effects such as nausea and diareah?

Varies greatly: It can be almost immediate if the medication is irritating to the lining of the stomach. However, one can develop nausea or diarrhea at any time while on antibiotics or even sometimes after finishing them. It takes about a year for healthy gut bacteria to fully return to normal after antibiotics, but amox generally isn't so hard on these bacteria and many experience no problems with it at all.