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Crayfishes (Decapoda) are common inhabitants of agricultural headwater streams in the Midwestern USA that have been impacted by physical habitat degradation and contamination by agricultural pollutants. The frequency and severity of injuries within crayfish communities are indicators of crayfish aggression, which is influenced by physical, chemical, and biotic factors. Previous studies have not evaluated the relationships of the frequency and severity of crayfish injuries with physical habitat quality, water quality, and biotic factors within agricultural headwater streams. Understanding these relationships will assist with determining if crayfish injury variables can serve as an indicator of physical habitat quality or water quality in these small degraded streams. We sampled crayfishes, documented the frequency and type of injuries, and measured instream habitat and water chemistry in 2014 and 2015 within 12 agricultural headwater streams in Indiana, Michigan, and Ohio. We documented five native crayfish species from 1641 adult captures. The most abundant species were Faxonius rusticus, Faxonius immunis, and Faxonius propinquus. Linear mixed effect model analyses indicated that four crayfish injury response variables were positively correlated (p < 0.05) with crayfish density, physical habitat quality, and water velocity diversity and that crayfish injury response variables were more strongly correlated with crayfish density than physical habitat quality or water quality. Our results indicate that response variables describing the severity and frequency of crayfish injuries can be effective indicators of physical habitat quality in agricultural headwater streams. [ABSTRACT FROM AUTHOR]