One key issue for theory in stream ecology is how much stream flow can be changed while still maintaining an intact stream ecology, instream flow needs (IFNs), the study of determining IFNs is challenging due to the complex and dynamic nature of the interaction between the stream environment and the biological community. We develop a process-oriented benthic-drift model that links changes in the flow regime and habitat availability with population dynamics. In the model, the stream is divided into two zones: drift zone and benthic zone, and the population is divided into two interacting compartments: individuals residing in the benthic zone and individuals dispersing in the drift zone. We study the population persistence criteria, based on the net reproductive rate R_0 and on related measures. We develop new theory to calculate these quantities and use them  to investigate how the various flow regimes, population birth rate, individual transfer rates between zones, and river heterogeneity affect population persistence. The theory developed here provides the basis for effective decision-making tools for water managers.