It appears that biofilms arrange their internal structure according to the flow velocity at which they are grown, which affects the internal mass transfer rate and microbial activity. In biofilms grown at various flow velocities we determined the vertical profiles of the local relative effective diffusivity (termed D(l)) at several locations within each biofilm. From these profiles we calculated the surface-averaged relative effective diffusivity (termed D(sa)) at various distances from the bottom and plotted it against these distances. The D(sa) decreased linearly toward the bottom, forming well-defined profiles that were different for each biofilm. The gradients of these profiles were multiplied by the diffusivity of oxygen, zeta = D(w) dD(sa)/dz, and plotted versus the flow velocity at which each biofilm was grown. The gradients were low at flow velocities below 10 cm/s, reached a maximum at a flow velocity of 10 cm/s, and decreased again at flow velocities exceeding 10 cm/s. The existence of a maximum indicates a possibility that two opposing forces were affecting the slope of the profiles. To explain these observations we hypothesized that biofilms, depending on the flow velocity at which they are grown, arrange their internal architecture to control (1) the nutrient transport rate and (2) the mechanical pliability needed to resist the shear stress of the water flowing past them. It appears that biofilms attempt to satisfy the second goal first, to increase their mechanical strength, and that they do so at the expense of the nutrient transfer rate to deeper layers. This strength increase is associated with an increase in biofilm density, which slows down the internal mass transport rate. Biofilms grown at low flow velocities exhibit low density and high effective diffusivity but cannot resist higher shear stress, whereas biofilms grown at higher flow velocities are denser and can resist higher shear stress but have a lower effective diffusivity.