This research study explores the relationship of urbanization to ecology in the wadeable streams of developing watersheds and describes a protocol, which urban stormwater management agencies can apply in their jurisdiction, to prevent the severe ecologic deterioration that presently occurs in urban streams as a watershed develops. The protocol comprises an 8-step process that involves data collection and analysis integrated with mathematical modeling of runoff from existing and proposed urban development to determine how biologic health indices such as the benthic index of biotic integrity (B-IBI) or Ephemeroptera, Plecoptera, Trichoptera (EPT) richness responds to urbanization of a watershed. Stormwater managers can apply this protocol in their areas of jurisdiction to assist them in developing urban runoff management rules and design criteria with some assurance that the resulting development will minimize negative impacts on the ecology of receiving streams. In addition to the full protocol, a simple protocol is also provided for municipal agencies to use that does not require extensive data collection.