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Benthic impairments indicate that a water body may not adequately support aquatic life. As of September 2001, 111 stream segments (732 km or 455 miles) in Virginia were included in its 303(d) list owing to benthic impairments and must undergo the TMDL process. The objective of this paper is to describe case studies on developing benthic TMDL reports for impaired stream segments in which the suspected pollutant source is effluent from trout farms. This paper describes the approaches and protocols used for the bioassessment, stream corridor assessment, and characterization of the trout farm effluents and nonpoint source load allocations utilized in the TMDL reports. The paper discusses the challenges to identify a linkage between water quality stressors and benthic degradation and the tasks to determine load reductions of the target pollutants to meet water quality goals in preparation of acceptable TMDL reports.