Variations in the depth of radar-detectable englacial layers (isochrones) are commonly used to assess past variability in accumulation rates, but little is known about the effect of internal and basal flow variations on isochrone deflections (e.g. bumps, troughs). In this paper, we show how the isochrones are affected by such variation using a three-dimensional flow model to investigate changes in the flow mode and in increased basal melting. We also investigate how transverse flows with lateral velocity gradients affect the development of isochrones. We use the model to visualize how such variations will be seen in radar lines which cross the flow direction. We show that in the presence of lateral gradients in the flow field we can produce bumps and troughs when viewed along transects perpendicular to the flow. The model results show that the influences of flow convergence, melting and changes in flow mode, when coupled together, affect isochrones over the whole depth of the ice sheet. Finally, changes in the near-surface layers cannot be solely attributed to spatial variation in the accumulation rate; there can also be a strong signal from changes in the flow mode.