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The Clean Water Act directs us to protect and restore the physical, chemical, and biological integrity of the Nations waters. Biological integrity has been defined as the ability of an aquatic ecosystem to support and maintain a balanced, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of natural habitats within a region. Florida has developed stream invertebrate-based bioassessment procedures, known as the Stream Condition Index (SCI) and BioRecon, which effectively determine the biological integrity of stream systems. Several anthropogenic factors, including degradation of water quality, hydrological modifications, and habitat impairment (especially sedimentation effects) adversely influence biological integrity. The bioassessment procedures, in conjunction with standardized habitat measurements (which include elements such as bank stability and sediment smothering) can provide evidence that sediments have contributed to an impaired ecological condition. Descriptions of the SCI, BioRecon, and habitat assessment procedures are provided, with emphasis on the evaluation of sediment effects. Examples of how these techniques can be used in tandem to assess both sediment sources (runoff from dirt roads) and effectiveness of Best Management Practices to control sediment (silviculture BMPs) are also presented.