Abstract. The development of accurate water quality modeling tools is necessary for integrated water quality management of river systems. Even though some water quality models can simulate dissolved oxygen (DO) concentrations accurately during high-flow periods and phytoplankton blooms in rivers, significant discrepancies remain during low-flow periods, when the dilution capacity of the rivers is reduced. We use the C-RIVE biogeochemical model to evaluate the influence of controlling parameters on DO simulations at low flow. Based on a coarse model pre-analysis, three sensitivity analyses (SAs) are carried out using the Sobol method. The parameters studied are related to bacterial community (e.g., bacterial growth rate), organic matter (OM; partitioning and degradation of OM into constituent fractions), and physical factors (e.g., reoxygenation of the river due to navigation and wind). Bacterial growth and mortality rates are found to be by far the two most influential parameters, followed by bacterial growth yield. More refined SA results indicate that the biodegradable fraction of dissolved organic matter (BDOM) and the bacterial growth yield are the most influential parameters under conditions of a high net bacterial growth rate (= growth rate − mortality rate), while bacterial growth yield is independently dominant in low net growth situations. Based on the results of this study, proposals are made for in situ measurement of BDOM under an urban area water quality monitoring network that provides high-frequency data. The results also indicate the need for bacterial community monitoring in order to detect potential bacterial community shifts after transient events such as combined sewer overflows and modifications in internal processes of treatment plants. Furthermore, we discuss the inclusion of BDOM in statistical water quality modeling software for improvement in the estimation of organic matter inflow from boundary conditions.