Individual plant cells have a genetic circuit, the circadian clock, that times key processes to the day-night cycle. These clocks are aligned to the day-night cycle by multiple environmental signals that vary across the plant. Thus, the clock may be set separately in cells creating discrepancies in timing. However, cells and tissues often must act in unison in order to time biological events appropriately. How does the plant integrate clock rhythms, both within and between organs, to ensure coordinated timing? To address this question, we developed an imaging method capable of monitoring the clock at the sub-tissue level across entire Arabidopsis thaliana seedlings. Consistent with previous tissue-level studies, our results showed that the clock runs at different speeds (periods) in each organ, which causes the clock to peak at different times across the plant in both constant environmental conditions and light-dark cycles. Closer examination revealed that spatial waves of clock gene expression propagate both within and between organs. A combination of modelling and experiment revealed that these spatial waves are the result of the period differences between organs and local coupling, rather than long-distance signalling. With further imaging experiments we showed that the endogenous period differences, and thus the spatial waves, can be generated by the organ specificity of inputs into the clock. We demonstrated this by modulating periods using light and metabolic signals, as well as with genetic perturbations. Finally, in the field, clocks entrain to complex environmental cycles. To begin to understand how clock’s respond to more natural light-dark cycles, we developed methods for imaging seedlings under more realistic light conditions. Preliminary results suggested altered spatial and temporal organisation amongst the core clock genes under more realistic light-dark cycles. Together, our results suggest that plant clocks can be set locally by environmental inputs, but coordinated via cellular coupling.