Monitoring and research strategies of the Long Term Resource Monitoring Program require a current, objective understanding of the factors that control ecological structure and function of floodplain reaches within the Upper Mississippi River System. The conceptual model presented here is designed to fill part of this need by listing major factors (abiotic and biotic) and disturbances (natural and human-induced) that operate at each of five spatial scales. In decreasing order of size, the spatial scales include: basin, stream network, floodplain reach, navigation pool, and habitat. Major factors are defined as those which act to keep ecosystem variables within predictable limits over a reference time period. A disturbance is an event that disrupts structure or function at the ecosystem, community or population level of biological integration. The conceptual model is meant to be dynamic, and sill be modified as new information becomes available, so that research and monitoring strategies can be adjusted annually in response to unanticipated resource problems.