Suspended sediment (SS) loadings in freshwater habitats have increased over the past century and SS is now a significant environmental stressor. Greater tolerance to environmental stressors has been proposed as a factor in the success of aquatic invasive species. Further, parasites may interact with environmental stressors to increase host susceptibility to loss of fitness and mortality. We compared the effects of SS exposure on the gill structure and aerobic scope of the endangered white-clawed crayfish (Au-stropotamobius pallipes), and the invasive signal crayfish (Pacifastacus leniusculus), and assessed impacts in relation to parasite burden. SS caused gill fouling and reduction in aerobic scope in both species, though A. pallipes was more susceptible than invasive P. leniusculus. The parasite Branchiobdella astaci, a crayfish worm that infests the gills, interacted with the sediment to affect gill structure whereas infection with the microsporidian parasite Thelohania contejeani had no effect on crayfish response to SS. Juvenile P. lenisuculus had a higher standard metabolic rate than A. pallipes, which may be linked to competitive advantages such as higher growth rate and behavioural dominance. Conservation of A. pallipes often involves relocation of threatened populations to isolated still-waters; our findings suggest that SS levels should be assessed before relocation.