As the global area devoted to urban uses grows, an increasing number of freshwater species will face imperilment due to urbanization effects. Management of these impacts on both private and public lands is necessary to ensure species persistence. Such management entails several hallenges: (1) development of a management policy appropriate to the stressors; (2) linking stressor levels to species population attributes; (3) forecasting the effects of alternative management policy decisions on the species, and (4) using adaptive management to adjust the policy in the future. We illustrate how these challenges were addressed under the Etowah Habitat Conservation Plan (Etowah HCP), a management plan for three federally protected fish species in Georgia, USA. The plan involved the creation of a management policy to address the impacts of the greatest stressor, stormwater runoff, as well as other stressors. Models were constructed to link population indices of the three species with a key indicator of stormwater runoff, effective impervious area (EIA). Then, models were applied to projected levels of EIA under full watershed buildout to fine-tune the parameters of the management policy. Forecasting indicated that the most sensitive species, the Etowah darter, was likely to decline by 84% in the absence of the Etowah HCP, but only 23% if the Etowah HCP were implemented. Although there was substantial uncertainty in model predictions, an adaptive management plan was established to incorporate new data and to adjust management policies as necessary.