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The Patuxent River watershed is a heavily impacted basin (2290 km 2 ) and estuarine tributary (120 km 2 ) of the Chesapeake Bay, USA. To assist management of the basin, we are testing a coupled modelling system composed of a watershed model (HSPF), an estuarine circulation model (CH3D), and an estuarine water‐quality model (CE‐QUAL‐ICM). The modelling system is being tested to guide the development of Total Maximum Daily Loads (TMDLs), and therefore errors in the models must be carefully evaluated. A comparison of daily total nitrogen (TN) concentrations simulated in HSPF with observations indicated that there was no significant bias, with an rms error of 37%. In contrast, modelled total phosphorus (TP) and total suspended solids (TSS) had significant bias with larger rms errors (65% and 259%, respectively). In the estuary, CH3D accurately simulated tides, temperature, and salinity. CE‐QUAL‐ICM overestimated nitrogen (N) and phosphorus (P) in the upper estuary and underestimated in the lower estuary, primarily because intertidal marshes are not currently a model component. Model errors declined from short (⩽1 day) to long (multi‐year) timescales as under‐ and overestimations cumulatively cancelled. Watershed model errors propagate into the estuarine models, interacting with each subsequent model's errors, which limits the effectiveness of this TMDL management tool at short timescales. [ABSTRACT FROM AUTHOR]