Competition between aquatic organisms is heavily influenced by abiotic factors in the environment, specifically flow regime in aquatic systems. Flow regime has been shown to significantly affect the way in which a species uses the environmental resources and alterations in flow can exasperate competitive advantages by congenerics. However, little work has concentrated on the competitive outcome between native and invasive organisms as a function of flow regime. Here, we sought to uncover how competition between two crayfish species (the native virile crayfish [Faxonius virilis] and invasive rusty crayfish [Faxonius rusticus]) was affected by varying flow rates. To do this, we size-matched crayfish and quantified three separate behaviors (food use, shelter use, and fights) of crayfish in four different discharge levels (no discharge—0 cm3/s; low discharge—116 cm3/s; intermediate discharge—345 cm3/s; high discharge—450 cm3/s). We found that the number of foraging bouts was significantly (p < 0.001) influenced by discharge levels for both species, where rusty crayfish foraged more often in no and discharge. The number of times crayfish sheltered also varied between species and was significantly (p < 0.001) altered by discharge level, where rusty crayfish sheltered more often in no discharge and virile crayfish sheltered more in low and intermediate discharge levels. Similarly, the number of fights that crayfish engaged in also significantly (p < 0.001) depended upon species and discharge levels. Rusty crayfish engaged in more agonistic activities in no and high discharge levels while virile crayfish participated most often in low and intermediate discharge levels.