Nearly 40% of the cropland in Great Lakes and Cornbelt states is drained to create arable farmland, so that much of their headwater stream network is comprised of ditches and drains. The two-stage ditch, sized to contain the 100-year flood but designed to allow development of benches and a more natural channel, is gaining attention as a stream restoration approach. To evaluate how channel configuration affects measures of ecological integrity, we selected 20 sites with (a) standard trapezoidal configuration, (b) observable natural bench development and (c) natural channels. Channel shape variability was least in trapezoidal channels, somewhat greater in benched channels and greatest in natural channels. Habitat quality was highest for natural sites and lowest for the trapezoidal drains. Fish taxon richness was surprisingly high at 36 species, and assemblages were dominated by 10 species that comprised 83% of the total collection and included intolerant as well as tolerant species. IBI scores were low (median =16 out of 100) and did not differ among stream types. Despite observable differences in habitat condition, fish assemblages were not obviously a function of in-channel habitat. Work continues to determine whether fish assemblages are the ephemeral reflection of propagule pressure or self-maintaining communities.