Conservation adequacy is defined as the ability of conservation measures to sustain biodiversity. Although river network connectivity is important for maintaining key ecological processes and ensuring persistence of biodiversity, it also facilitates the propagation of threats along river networks, which may compromise the sustainability of freshwater biodiversity and therefore conservation adequacy. This study aims to introduce two modifications to river conservation planning related to connectivity and catchment condition that together can improve the adequacy of the priority areas identified. This will establish an operational framework for end-users, such as policy makers and NGOs. We operationalize the connectivity framework that has recently emerged in systematic river conservation planning by using a GIS coding system for catchment location in the conservation software package marxan. Additionally, we use a landscape measure of catchment disturbance to direct the conservation plan to the least-disturbed area while still meeting targets for the conservation of fish species used as surrogates for overall biodiversity in our study catchment, the Daly River in northern Australia. This proxy for condition aggregates information on land-use, extractive industries, point-source pollution, and water infrastructure. We successfully modelled the distribution of 39 fish species based on GIS-derived landscape descriptors (most important descriptors were; discharge, distance to river mouth, geology and conductivity). Results from the systematic planning analysis identified a portfolio of watersheds that delivered close to optimal upstream protection with around 4700 stream kilometres (30% of the total network). When using upstream disturbance as an extra penalty, most of the network stayed intact; however, a replacement area was found for a major tributary, which only added an extra 1% of the stream network to the total area. Synthesis and applications. Improving conservation adequacy by accounting for upstream connectivity and condition using this easy-to-implement framework and software package has the potential to facilitate further application of systematic methods in river conservation planning. Furthermore, integrating condition as a discounting factor can also improve conservation adequacy in a broad range of environments (including terrestrial and marine), while not necessarily increasing the management costs.