Modified and artificial channels present a challenge for watershed managers charged with protecting aquatic life and related beneficial uses in urban or agricultural settings while also providing flood protection or water conveyance. To help watershed managers incorporate wadeable modified channels into regulatory or management programs, we have developed a framework for interpreting indicators of biological condition and eutrophication. First, we created a reach classification system based primarily on bed and bank material. For each class of streams and each bioassessment index, we evaluated the range of indicator values and responsiveness of benthic macroinvertebrate and algal indices to water quality or habitat stress indicators. We determined that the invertebrate index rarely (<10% frequency) attained good scores in hard-bottom channels, but regularly did so in soft-bottom channels, whereas algal indices showed the opposite pattern. We evaluated statistical distributions that managers could use as assessment benchmarks based on “best observed” conditions in each channel class, and developed eutrophication response models to identify levels of biostimulatory substances (nitrogen, phosphorus, and benthic algal biomass) associated with these benchmarks. This framework provides regulators with a technical foundation for setting goals in modified channels where reference expectations may not be achievable as long as modifications remain in place.