Human-induced alteration of the natural flow regime is a major threat to freshwater ecosystems and biodiversity. The effects of hydrological alteration on the structural and functional attributes of riverine communities are expected to be multiple and complex, and they may not be described easily by a single model. Based on existing knowledge of key hydrological and ecological attributes, we explored potential effects of a flow-regulation scenario on macroinvertebrate assemblage composition and diversity in two river systems in Australia's relatively undeveloped wet-dry tropics. We used a single Bayesian belief network (BBN) to model potential changes in multiple assemblage attributes within each river type during dry and wet seasons given two flow scenarios: the current, near-natural flow condition, and flow regulation. We then used multidimensional scaling (MDS) ordination to visually summarize and compare the most probable attributes of assemblages and their environment under the different scenarios. The flow-regulation scenario provided less certainty in the ecological responses of one river type during the dry season, which reduced the ability to make predictions from the BBN outputs directly. However, visualizing the BBN results in an ordination highlighted similarities and differences between the scenarios that may have been otherwise difficult to ascertain. In particular, the MDS showed that flow regulation would reduce the seasonal differentiation in hydrology and assemblage characteristics that is expected under the current low level of development. Our approach may have wider application in understanding ecosystem responses to different river management practices and should be transferred easily to other ecosystems or biotic assemblages to provide researchers, managers, and decision makers an enhanced understanding of ecological responses to potential anthropogenic disturbance.