In response to water quality standard violations linked to excessive organic matter (OM) and a lack of sampling data informing the Total Maximum Daily Load (TMDL), an organic matter budget was created to quantify and identify sources of OM in the lower Jordan River (Salt Lake City, UT). By sampling dissolved, fine, and coarse particulate OM, as well as measuring ecosystem metabolism at seven different sites, the researchers aimed to identify the origin of excess OM, and understand pathways by which different size classes of the OM pool are generated. The dissolved fraction (DOM; 94 %) was found to be the dominant form of OM transported within the river with fine particulate organic matter (FPOM; 6 %) the second most abundant, and coarse particulate organic matter (CPOM; 1 %) transport relatively insignificant in the overall OM budget. Primary production exceeded respiratory losses in the upper river, and this, along with OM inputs from two tributaries (where water reclamation facilities discharge into the river) delivered excess OM to the impaired lower reaches. Increasing stream metabolism index (SMI) with distance downstream (>1 in the lower river) further demonstrated that transport of excessive organic matter into the lower river was from upstream sources and not due to lateral inputs. This simple approach to characterizing the organic matter budget as it relates to water quality in the Jordan River was effective and could serve as a model for future studies attempting to quantify and identify sources of OM in urban ecosystems.Keywords Water quality impairment . Organic matter budget . Urban stream syndrome Urban Ecosyst (2016) 19:1623-1643 DOI 10.1007 A TMDL study defines the relationship between pollutant sources and in-stream water quality conditions. Based on this relationship, a permissible load is defined that will result in meeting state water quality standards and restore aquatic life beneficial use support for impaired segments of the river (UT DWQ 2012).