In this talk I describe various problems involving the intersections of fluid mechanics, bacterial biofilms and physical chemistry. I first highlight our studies of the influence of fluid motion on surface-attached bacteria and biofilms, where we identify and characterize upstream migration of surface-attached bacteria in a flow. Second, I highlight the influence of flow on quorum sensing, which refers to bacterial communication and collective behavior regulated by secreted chemicals. Our results suggest that bacterial colonization and biofilm development under flow can lead to heterogeneous QS activation, which promotes diversity in the genetic programs that bacteria enact. As a consequence, genetically identical bacteria exhibit different behaviours at particular regions and at particular times under flow. Finally, I describe an out-of-equilibrium consequence of concentration gradients, which, perhaps surprisingly, allow movement of particles (e.g. vesicles, DNA) in simple geometries. In particular, with salt gradients, via a mechanism referred to as diffusiophoresis, we can remove particles from dead-end pores or deliver particles into such pores. We explore the phenomenon using experiments and modeling. We close by posing the question if there might be broader consequences of these out-of-equilibrium physical chemistry ideas in biological contexts.