The present contribution focuses on modeling the total particulate organic carbon (POC) and benthic POC transport from a lowland stream impacted by agricultural land-use. A mass balance, reach scale model is verified that accounts for water, sediment and POC transport, sediment and POC temporary storage and exchange with the streambed, and production and degradation of carbon pools in the benthos. We found that the POC load is highly variable during individual hydrologic events and is influenced by transport of mixed carbon sources including upland, streambank and benthic POC sources. Benthic POC stocks and transport were found to vary seasonally and annually but are in a state of long-term equilibrium. Equilibrium is governed by negative feedback mechanisms whereby high POC export due to extreme hydrologic events and high-frequency hydrologic events reduces benthic POC stocks and inhibits benthic POC growth. Benthic POC accounted for 4 tC y−1 or 22% of the total annual POC loading in the stream's main stem and 8.9 tC y−1 or 48% of the POC yield for the entire watershed. These results suggest that further attention should be given to benthic-derived POC when budgeting stream ecosystem carbon for low-order stream systems. Copyright © 2012 John Wiley & Sons, Ltd.