Headwater stream networks comprised of ditches and drains are prevalent in the Great Lakes and Cornbelt states, where 37% of the cropland has been drained to create arable land. The two-stage ditch, an alternative to the typical trapezoidal construction of agricultural drains, is gaining attention as a stream restoration approach compatible with production agriculture. In the two-stage ditch, a narrow channel is constructed within a wide vegetated drain to mimic the dimensions of a more natural stream channel and allow for bench development in a surrounding miniature floodplain. We studied agricultural drains with varying degrees of bench development to compare the biological communities of drains with the standard trapezoidal configuration to those with narrowed channels and naturally formed benches. Agricultural drains were also compared to reference stream sites. Canonical correspondence analysis identified multiple environmental variables associated with fish and invertebrate communities of agricultural drains. Bench development was associated with fish species assemblages and invertebrate community metrics, though not with fish community metrics or invertebrate species assemblages. Reference streams differed from drains only in the proportion of insectivorous fish and the proportion of Ephemeroptera, Plecoptera, and Trichoptera invertebrates.