Patterns of connectivity are critical to structuring both spatial and temporal variation in the composition of species populations and assemblages. Water resource development has an important impact on longitudinal connectivity in rivers, and disrupts natural patterns of dispersal of individuals between segments of the river network. Consequently, artificial barriers alter the structure, size and distribution of species populations leading to impacts on aquatic biodiversity. * Quantitative assessment of the ecological effects of connectivity alteration is necessary to develop effective conservation plans to manage the impacts of anthropogenic fragmentation. Connectivity alteration is a complex environmental disturbance because the potential scale of impact is dependent on the spatial scale at which biota undergo life-history processes such as spawning and recruitment. Few river networks have single migration barriers, meaning that multiple points of fragmentation are present and have potentially interacting effects. Therefore, conventional 'control-impact' approaches to impact assessment may be inappropriate or confounded. Furthermore, monitoring patterns of fish population or assemblage structure moving through fish passage facilities alone creates a mismatch between the spatial scale of impact and assessment of water resource development. * This paper uses a case study in subtropical Australia to highlight three potential approaches to increasing inference of the impact of fragmentation by barriers on riverine fish. Thorough understanding of life-history and dispersal ecology of fish is necessary to understand and predict the consequences of fragmentation, and comparing patterns of distribution among species with different migration requirements can identify sources of fragmentation. Monitoring patterns in fish assemblages at both the barrier and river network scale increases the strength of inference of the effects of connectivity alteration and management. Experimental removal of artificial barriers would assist in determining the effect of fragmentation by restoring connectivity. Such approaches would improve predictions of connectivity management and underlying drivers of aquatic biodiversity.