We completed a three-year pre-construction monitoring plan of two Pennsylvania streams that encompassed measurements of biotic communities and physicochemical variables in order to evaluate the future effectiveness of a planned natural stream channel restoration project designed to reduce stream erosion, sedimentation and nutrient influx. To meet this objective we assessed forested (control) and impaired sites in the South and East Codorus Creek branches within the Susquehanna River watershed. Our pre-restoration data support that the fish communities were significantly different between sites evidenced by the lower number of parasitized fish, greater biomass, and greater numbers of salmonids (10 fold increase) and other pollution intolerant fish at the control sites. The higher total phosphorus concentrations and suspended sediments in the impaired sites mostly likely explain the low number of pollution intolerant species and the need for restoration in these impaired areas. The lack of significant differences in either diversity or evenness between the control and impaired sites stresses the importance of why fish communities and overall stream ecosystem health are assessed by the calculation of multiple metrics.