The hyporheic zone of lotic ecosystems has become the focus of renewed research interest because it is an important link between surface waters and the aquifer. Historically, research in the hyporheic zone has been more narrowly focused by those interested in that region as a refugium for insect and other macroinvertebrate fauna (the hyporheos) or as a location for salmon spawning. As paradigms and perspectives in lotic ecology have evolved, and have expanded to include studies of streambeds as sites of processing, transport, and storage of solutes and organic matter, the hyporheic zone once again has become the focus of research efforts on interactions between hydrology and biology which occur there. One of the more recent interests in the hyporheic zone is of surface water-groundwater interaction, strongly implied by descriptive studies and quantified by field manipulations. The importance of groundwater inputs of nutrients and dissolved organic carbon to streams and the processing of these solutes within the hyporheic zone have been acknowledged. And for those who have compared and contrasted stream water and groundwater both chemically and microbially, more indepth studies of the hyporheic zone within some hydrologic context may put these comparisons into clearer perspective. Along the course of a stream, the cumulative effects of interaction and exchange of groundwater and surface water within the "interface zone" of hyporheic zone may be reflected downstream in surface water quality, depending on the substance(s) in question. There may be a longitudinal zonation of hyporheic zones along the upstream-to-downstream continuum as postulated for surface waters by the River Continuum Concept of Vannote et al. The main study site was on the East Branch of the Maple River, a warm-water, nutrient-poor stream in northern Michigan which drains Douglas Lake. The primary geomorphological unit in the stream was the riffle-pool sequence. The substratum consisted of medium sand. Groundwater and surface water were easily differentiated in this system by temperature. Based on this simple technique, we were able to map temperature profiles and hypothetical subsurface (hyporheic) flow paths through a hyporheic zone. Mapping the physicochemical properties and biological characteristics helped delineate the hyporheic zone in this system and lay the groundwork for further ecological studies. Each of the ensuing four chapters addresses a distinct idea in hyporheic ecology. Chapter II is primarily descriptive, and focuses on spatial and temporal patterns in physicochemical characteristics of a hyporheic zone, with comparisons to groundwater and surface water. Physicochemical gradients resulting from mixing and exchange of surface water and groundwater along the longitudinal hydraulic gradient of a hyporheic zone have not been examined, which makes this chapter a unique contribution to the limited body of knowledge existing thus far. Chapter III focuses on a detailed study of the temperature patterns beneath Chara hummocks, a biological feature of the streambed which can augment or alter expected underflow gradients discussed in Chapter II. The advantages that subsurface gradient alterations offer to surface-dwelling organisms remains virtually unstudied. The fact that alterations occur and have been documented for a number of bed surface objects is a unique aspect of hyporheic ecology and lotic perspective. Chapter IV is an investigation of the bacterial communities along the hyporheic physicochemical and hydraulic gradient discussed in Chapter II. Included are spatial and temporal variabilities in abundance, biomass, metabolic activity, and productivity. Chapter IV also presents results of experimental manipulations to test metabolic and growth responses to different "qualities" of DOC thoretically expected along the physicochemical gradients. Each of the chapters is related by a common perspective: that the subsurface environment of the streambed is coupled to both the surface water and groundwater environments in ways which are more amic and complex than formerly thought. Further, there are regions in the streambed where surface water downwelling and hyporheic water upwelling are predictable, which implies mixing of the two water masses alogn longitudinal subsurface flow paths. These regions present organisms with a set of conditions which may be quite variable (more characteristic of surface waters) or relatively stable (more groundwater-like) depending on their location within the streambed. Chapters II, III, and IV are coupled by exploring this link between hydrology and hyporheic biology in Chapter V.