Hi,

I assume you are running sybr green dye based qPCR reaction. You can confirm presence of primer dimer by doing post pcr melt curve analysis. Run PCR with NTC and positive control and check melt curve peaks. You can also check primer dimer by running PCR product on agarose gel.

Run out your samples on an agarose gel. Contamination will show the same size product as your positive control, primer dimers will be much smaller. Some primers tend to form dimer product more easily than others. You may need to adjust the amounts of each primer in your reactions.

Good luck!

Hello

Katie A Burnette and Ajith Kumar are right. Also the source of contamination may not be only water! In this case I would have made a fresh master mix, freshly made primers and ... use filter tips for a while if possible, to eliminate any source of contamination.