The use of non‐lethal experiments to elucidate behavioural and physiological thresholds to environmental stressors can provide valuable data for identifying threats to, and critical habitat of, imperilled species. Increased turbidity contributes to population declines and loss of fish diversity globally, but the complex direct and indirect effects of this stressor on imperilled species are not well understood. Response to turbidity was examined in a group of closely related North American fishes (Notropis spp.), including four imperilled shiners: pugnose shiner (N. anogenus), bridle shiner (N. bifrenatus), blacknose shiner (N. heterolepis), blackchin shiner (N. heterodon), and the more common mimic shiner (N. volucellus). Two experiments quantified (i) the behavioural response of each species to progressively increasing turbidity, and (ii) critical swimming speed of fishes acclimated in turbid‐ and clear‐water treatments to provide insights into effects of low turbidity on aerobic performance. Very low levels of turbidity (<10 NTU) altered schooling behaviour of pugnose and bridle shiners, both imperilled. Critical swimming speed was lower in pugnose shiner acclimated to low turbidity than fish acclimated to clear waters, while the opposite pattern was observed in bridle shiner. Low turbidity did not affect behaviour or critical swimming speed in the other three shiner species, suggesting that they are more tolerant of low levels of turbidity. The demonstration of alterations in ecologically significant measures of behaviour and performance in the pugnose and bridle shiners, provides evidence required to identify and implement conservation and recovery actions related to turbidity of human origin. In addition, it is suggested that species‐specific responses should be evaluated, where possible, when defining critical habitat. Copyright © 2014 John Wiley & Sons, Ltd.