Historically, physical, chemical, and biological processes have largely been considered independently in both engineered and natural water systems, but synergies between fluid flow, particle motion, biogeochemical transformations, and microbial metabolism and growth control a wide array of critical processes in both natural and engineered systems.  Surface waters and groundwaters have long been considered to represent distinct systems with little connectivity.  However, coupling between hydrologic and geomorphic processes causes surface and subsurface waters to be highly connected over a wide range of scales.  This connectivity drives substantial exchange of suspended matter between rivers and underlying groundwater, including continuous deposition and resuspension in river beds. This exchange increases opportunity for interaction of stream-borne material with underlying sediments, which is expected to alter the hydrogeological properties of fluvial deposits, control redox zonation and associated biogeochemical transformations in the subsurface, and increase the opportunity for metabolism of terrestrial particulate organic matter in rivers. Similar dynamics drive the migration of microorganisms, making surface-groundwater interactions a key process in both microbial ecology and waterborne disease transmission.  Finally, it has recently been recognized that most submerged surfaces become coated with microbial biofilms, yielding complex physical/chemical/biological interfaces.  Microbial growth in biofilms and riverbeds share several essential features:  growth at an interface leading to development of strong internal transport limitations and chemical gradients that produce a high degree of habitat heterogeneity. This leads to general recalcitrance of biofilms to biocides and other chemical stresses, producing persistent colonization of surfaces in water systems even when subject to water treatment measures.