Geology and precipitation interact to determine the geomorphology of a stream basin. We propose that stream geomorphology in turn interacts with sunlight, air temperature, precipitation, and geology to produce a distribution of environmental drivers (incident radiation, discharge, water temperature, nutrients) that is largely responsible for determining the distribution of organisms in streams. GEOMOD, a physically explicit stream ecosystem model, was designed to examine this proposal. The model has a geomorphically based hierarchical structure with basin, reach, and channel-unit levels of resolution. We used GEOMOD: 1) to simulate annual cycles of the biota in 3rd- and 5th-order stream sections at the basin level of resolution and 2) to predict organism distributions at the reach and channel-unit level of resolution. Stream physical structure and the 4 environmental drivers were the only factors that differed among the sites. Data from two 150-m sections of 3rd-order Mack Creek (one in old-growth and the other in clear-cut forest) and from a 1.5-km section of 5th-order Lookout Creek in the Cascade mountains of Oregon were used to parameterize the physical structure and initial standing crops and calibrate the drivers. Uniform parameters were determined by curve-fitting. GEOMOD simulated annual magnitudes and cycles for abiotic (e.g., channel dimensions, fine particulate organic matter) and biotic (e.g., algae, invertebrates, fish) variables in Mack and Lookout creeks. With explicit parameterization of reach and channel-unit sequences, GEOMOD also predicted the distribution of organisms among channel units and reaches. Fish distributions were accurately predicted at the reach scale, while algal-invertebrate interactions and scouring effects became clear only when examined at the channel-unit level. These results demonstrate that organism distributions and interactions in highly structured streams such as those in the Pacific Northwest region of the USA can be effectively simulated with a physically explicit model. Although more complicated to design and parameterize than a uniform physical representation, a physical explicit model can be tailored to represent a wide variety of stream types.