The Grand Calumet River is an industrial river and a Great Lakes Area of Concern in southwestern Lake Michigan, USA. Recovery end points require well-formulated designs to assess the use of occurrence of internal and external anomalies, fluctuating asymmetry, and population indicators to determine recovery from the water-quality Beneficial Use Impairments of fish tumors and deformities. A paired-watershed approach using three reaches within the study area was sampled weekly and separated into near- and far-field reaches, whereas the Little Calumet River, Indiana Dunes National Lakeshore, served as a control. Field-collected Pimephales notatus were inspected for occurrence of deformities, erosion, lesion, and tumor (DELT) anomalies, measured for body symmetry, and dissected to ascertain sex and the condition of internal organs. Morphometric measurements (p ≤ 0.000), internal organ conditions (p = 0.001), and sex ratios of the fish (p = 0.001) were significantly different between the control and P. notatus test populations. The near-field individuals had the highest incidence of DELT occurrence (70 %) followed by the far-field reaches at Roxana Marsh (45 %) and Kennedy Avenue (41.9 %). Morphometric analysis showed significant differences between body size and shape and age class structure between populations. No test-reach individual lived to reach age >2 years. Gonads and livers from Grand Calumet individuals were found to be blackened, ruptured, and decreased in thickness. None of the fish from test study reaches displayed sexual structure in a 1:1 ratio. High sediment-contaminant concentrations for polycyclic aromatic hydrocarbon metals in the Grand Calumet River correlated (r (2) = 0.998) with decreased population fitness and decreased individual reproductive health.