In-channel persistent surface water provides critical refuge habitat for aquatic organisms in intermittently flowing rivers. Quantifying the flows that maintain connectivity among persistent waterholes is important for managing river flows to maintain refuges, improve their quality and facilitate connectivity and nutrient and energy transport. This study aimed to quantify spatial and temporal waterhole persistence and connectivity in a 664km reach of the Darling River in Australia's Murray-Darling Basin. A 35-year satellite imagery record and graph theory were combined to produce a time series of spatial graphs. Persistent in-channel waterholes represented nodes on the graph, with vertices reflecting connectivity during flow events. Models were developed to quantify temporal variation in connectivity in relation to environmental predictors at a reach scale and at specific waterholes. Connectivity was highly spatially variable and clearly impacted by flow interception at in-channel weirs. Several highly connected waterholes were identified as both hub and stepping stone habitats in the connectivity analysis, indicating that they may serve important ecological functions for both local and large-scale fish dispersal. Flow was the most influential predictor of reach-scale connectivity, followed by local rainfall. An analysis of specific waterholes found that following a reconnecting flow event, flow above the 75th percentile was required to maintain full connectivity of the most disconnected/isolated waterhole. This study demonstrated that connectivity can be predicted using variables including flow, rainfall, and antecedent climate conditions, thereby highlighting the usefulness of this technique for predicting connectivity under a range of flow scenarios.
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