Normal joint morphogenesis requires mechanical activity during development. Loss of mechanical strain causes abnormal joint development, which can impact long term joint health. While proliferation and changes to cell orientation are known to shape the joint, dynamic imaging of a developing joint in vivo has not been possible in other species. Using genetic labelling techniques in zebrafish such as photo-conversion of kaede and multi-spectral Zebrabow transgenic lines we were able, for the first time, to dynamically track cell behaviours in intact moving joints of individually labelled larvae. We identify that joint cell proliferation and migration, which contribute to normal joint morphogenesis, are mechanically controlled and are significantly reduced in immobilised larvae. By comparison to strain maps of the developing skeleton we identify canonical Wnt signalling as a candidate to transduce the mechanical forces into cell behaviours in the developing joint. We show that in the jaw Wnt signalling is reduced specifically in regions of high strain such as the interzone and developing ligaments, in response to loss of muscle activity through immobilisation. By pharmacological manipulation of canonical Wnt signalling we demonstrate that Wnt acts downstream of mechanical activity and is required for correct joint patterning and chondrocyte maturation. Knockdown of Wnt16 alone, leads to loss of Wnt response specifically in joint associated tissues. Finally, we demonstrate that Wnt16, independent of muscle activity, controls joint cell proliferation and migration, but plays no role in chondrocyte intercalation.