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Barriers to migration are a major threat to freshwater fish populations. A novel measurement of swimming speed performance and an analytical model were used to calculate the probability that endangered Macquarie perch, Macquaria australasica Cuvier, can swim through instream structures. Over the range of river discharges (2.7–166 ML day⁻¹) and temperatures (10–22 °C) examined, M. australasica could successfully pass through a rock‐ramp fishway and nearby natural riffles under most river discharges, whilst pipe culverts were passable only to large individuals (>17.7 cm total length) under a high river discharge. Cold water temperatures (below 16 °C) significantly reduced the likelihood of passage in each case. It was concluded that both the volume and thermal characteristics of environmental flow releases should be considered when assessing and remediating potential instream barriers to fish …