We examine the effect of disc topography and time modulation of the liquid flow rate at the inlet on the dynamics of a thin film flowing over a spinning disc. We use a combination of boundary-layer theory and the Karman-Polhausen approximation to derive coupled equations for the film thickness, and radial and azimuthal flow rates. Substrate patterning is taken into account in the limit of small-amplitude topography. Our numerical results indicate that the combined effects of flow rate modulation at the inlet and disc patterning can lead to a significant increase in interfacial waviness, which greatly exceeds that associated with the constant flow rate, smooth disc case. (C) 2008 Elsevier Ltd. All rights reserved.