The rivers of northern Australia are relatively pristine; supporting diverse and productive aquatic species and ecosystems of great social, cultural and economic value. Recent economic expansion places these rivers under profound and immediate threat; with increased water extraction and dam construction planned throughout the region. Water extraction will occur mostly during the dry season when flows and resources are at their lowest as habitats contract and potentially disconnect. The aquatic biota maybe adapted to the predictable low flow period but reduced dry season flows may result in chronic long term impacts, or the exceedance of critical flow thresholds that could have acute effects on a river’s ecology. Understanding these potential impacts is needed to inform Water Allocation Plans intended to maintain the ecological integrity of these rivers. We will present our current understanding of potential impacts based on reviewing the local and international literature, and present new conceptual models we have developed specifically for both perennial and ephemeral rivers of the wet-dry tropics. We will use these conceptual models to formulate research questions and potential monitoring indicators.