Swimming microorganisms employ a variety of apparatus to swim, leading to interesting biased trajectories in flows. As well as the potential for cells to influence their environment by large scale hydrodynamic instabilities, a typical strategy is for cells to associate with surfaces, leading to biofilms that are resilient to possibly hostile conditions. I shall present some visualization and modelling of flows around nascent biofilms in a channel. Cells not stuck to surfaces are driven by shear and are subject to local and external torques and stimuli. The dispersion of a suspension of swimming cells in a channel will be described, scaling up from individual swimming dynamics to suspensions: even non-biased swimming cells drift relative to the mean flow. Finally, I will discuss the non-intuitive transport of swimming cells in oscillatory flows due to helical resonant alignment.