Biofilms are complex mixtures of microorganisms and extracellular matrix that exist on many wetted surfaces. Recently, magnetic resonance microscopy has been used to measure fluid velocities near biofilms that are attached to the walls of capillary channels. These velocity measurements showed unexpectedly high secondary velocities (i.e., high velocity magnitudes perpendicular to the direction of bulk flow and perpendicular to the surface that the biofilm is attached), and the presence of high secondary velocities near a biofilm could increase the delivery of substrates to the biofilm. A mathematical model, based on the immersed boundary method, is used here to examine the physical interaction between a biofilm and a moving fluid in a capillary and to analyze possible factors that may contribute to the elevated secondary velocities observed experimentally. The simulation predicts the formation of a recirculation downstream of a biofilm, and this recirculation deforms and lifts the biofilm upward from the surface to which the biofilm is attached. Changing the mechanical properties (i.e., stiffness) of the biofilm impacts both the lifting of the biofilm and the magnitude of the secondary velocities. The maximum lifting of the biofilm occurs when the biofilm properties are similar to previous experimental measurements, which indicates that the mechanical properties of the biofilm may be tuned for the generation of maximum secondary velocity magnitude and transport of substrates to the biofilm. Biotechnol. Bioeng. 2011;108: 1893-1899. (C) 2011 Wiley Periodicals, Inc.