We describe the ecology of off-channel or "lateral" habitats as key attributes of the Shifting Habitat Mosaic (SHM) of a river flood plain at the Nyack Research Natural Area in northwestern Montana. Our working hypothesis was that lateral habitats are important to the cycling of energy and materials within the SHM and contribute greatly to the productivity and biodiversity of the floodplain ecosystem. We produce a quantitative description of temperature variation across aquatic and terrestrial habitats at Nyack. Thermal patterns across lateral habitats indicate vast differences exist between lateral habitats in habitat suitability for aquatic organisms over an annual cycle. Existing thermal regimes favor life history diversification. We further document the impacts of flood disturbances on organic matter accumulation by aquatic primary producers in off-channel environments. We were able to show that the annual flood pulse disturbance was the major force controlling periphyton community biomass, nutrient status, and species composition, with secondary control by surface and groundwater mediated water chemistry fluctuations during lower flow periods. We end with a study relating biodiversity pattern and process to lateral habitat heterogeneity. Data supported our prediction that densities and diversity of organisms and food webs of the flood plain would be greatly increased if off-channel habitats as well as main channel habitats were included. Collectively, lateral habitats uniquely support 50% of the total documented aquatic biodiversity of the entire floodplain. We conclude that lateral habitats contribute significantly to the biocomplexity of alluvial floodplain ecosystems.