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We monitored water quality in the Chattooga River Watershed (NE Georgia, NW South Carolina, and SW North Carolina) to compare sediment TMDLs with observed water quality. A judicial consent decree required the EPA to establish TMDLs in one year. The EPA was unable to fully characterize the sediment budgets of these streams and consequently issued phased sediment TMDLs which can be revised because information on the actual contributions of sediment to the Chattooga River Watershed from both point and nonpoint sources will be much better characterized in the future. The EPA listed streams as sediment impaired based upon aquatic indicator species data and relied upon total suspended solids (TSS) data and modeling to establish the sediment TMDLs. We found that TSS concentrations do not reflect mineral sediment concentrations because the organic and mineral components of TSS were highly variable between streams. TSS in forested streams could get quite high and were largely organic whereas TSS in streams more heavily impacted by land use change and roads were mostly mineral sediment. TSS and mineral sediment in a stream listed as being sediment impaired were significantly lower than streams listed as being only threatened. We also monitored bed material transport and sampled sediment mineralogy on one of our study streams. The sand and fine gravel in this stream were very dynamic. In-stream scour and deposition occurred frequently. No in-stream deposition occurred during small events; when road runoff was negligible. During larger events, road runoff and in-stream sediment deposition occurred. This suggests that the existing sediment TMDLs may not address the causes of sediment impairment of the aquatic ecosystems. The EPAs issuance of phased sediment TMDLs was insightful because it acknowledged our lack of understanding of the impacts of land usage and sediment dynamics on streams in the Chattooga River watershed.