A specially designed net was used to study fish entrainment and injury through towboat propellers in 13 pools of the Upper Mississippi and Illinois rivers. The net was attached to the stern of a 48.8‐m‐long towboat with twin propellers (in Kort propulsion nozzles), and sampling typically took place while the towboat pushed 15 loaded barges upstream at a time. In total, 254 entrainment samples over 894 km of the 13 study pools were collected. The sampling efforts produced 16,005 fish representing 15 families and at least 44 species; fish ranged in total length from 3 to 123 cm, but only 12.5‐cm or longer fish were analyzed because smaller fish could escape through the mesh of the trawl. Clupeidae (68% of total catch) and Sciaenidae (21%) were the dominant families. We detected no effects of towboat operation variables (speed and engine [i.e., propeller] revolutions per minute [RPM]) on entrainment rate (i.e., fish/km), but entrainment rate showed a wedge‐shaped distribution relative to hydraulic and geomorphic characteristics of the channel. Entrainment rate was low (<1 fish/km) in wide sections of the river, deep water, and swift current (or time periods characterized by faster flow); however, entrainment in narrow sections with shallow, slow water was highly variable and occasionally reached high levels (>30 fish/km). Although total entrainment rate was not related to engine RPM, the probability of being struck by a propeller increased with fish length and engine RPM. Limits on engine RPM in narrow, shallow, and sluggish reaches could reduce entrainment impact, particularly for large‐bodied fish.