Ecological theory predicts that the relative importance of benthic to planktonic primary production usually changes along the rivers' continuum from a predomination of benthic algae in lower stream orders to a predomination of planktonic algae at higher orders. Underlying mechanisms driving the interaction between algae in these habitats, its controlling factors and consequences for riverine ecosystems are, however, only partly understood. We present a mechanistic analysis of the governing ecological processes using a simplified, numerical model and examine how abiotic factors and biotic interactions influence benthic and planktonic algae by changing resource competition. We compare the outcome of the model with the results of a factorial mesocosm experiment mimicking the parameter spaces of the model. The results show a remarkable similarity with regard to the temporal development of benthic and pelagic algal biomass and shifting dominance patterns. In particular we analyse the effects of the pathways of nutrient supply (upwelling from the hyporheic zone, direct supply to the surface water, or via both pathways) and grazing in a gradient of river depths. Our results show that detachment of benthic algae, sinking of planktonic algae and the pathway of nutrient supply are key processes determining the respective algal biomass distributions particularly in shallow and intermediate deep systems. Increasing nutrient supply increases algal biomasses, but does not change the general pattern of the interactions. Decreasing light supply decreases the dominance of planktonic algae, but increases dissolved nutrients. At intermediate to high grazing rates algal biomass can be controlled by grazers, but however, at high grazing rates, dissolved nutrients accumulate in the surface water. Our results indicate that nutrient pathways, resource competition and internal control by grazing need to be considered explicitly for the understanding and explanation of eutrophication phenomena in riverine ecosystems. As a consequence, ecologically effective eutrophication management of running water systems has to go beyond the control of nutrient emissions or the achievement of limiting threshold values in the receiving waters, but requires the consideration of the nutrient pathways (surface water versus groundwater) and the shifting biological controls from lower to higher order stream ecosystems.