The effects of biomanipulation through eradication of benthic omnivorous fish species on benthic macroinvertebrate fauna were investigated in three tributaries of Bowman-Haley Reservoir, North Dakota, USA. Fish were eradicated with rotenone from the lower sections of each tributary. Adult common carp (Cyprinus carpio L) constituted over 95% of the fish killed by weight. Barrier fences were installed to prevent adult fish from repopulating the fish-free stream sections during summer. Benthic macroinvertebrates were monitored from one month before to three months after each rotenone application both upstream and downstream of the fish barriers. Also, in the second year of the study, three 8 m × 8 m fish exclosures were constructed, one near the mouth of each stream. Benthic invertebrate samples were collected inside and outside of exclosures for approximately two months after their installation. After fish eradications in two successive years, chironomid densities increased up to 50-fold in the fish-free areas but remained low elsewhere. Chironomid length and taxa richness increased upstream of the fish barriers. In areas where submerged vegetation became established after carp removal, benthic community richness increased compared to non-vegetated, fish-free areas. Chironomid densities also increased within the exclosures but remained lower than upstream of barriers.