Hydrodynamic models are useful tools for urban water management. Unfortunately, it is still challenging to obtain accurate results and plausible uncertainty estimates when using these models. In particular, with the currently applied statistical techniques, flow predictions are usually overconfident and biased. In this study, we present a flexible and relatively efficient methodology (i) to obtain more reliable hydrological simulations in terms of coverage of validation data by the uncertainty bands and (ii) to separate prediction uncertainty into its components. Our approach acknowledges that urban drainage predictions are biased. This is mostly due to input errors and structural deficits of the model. We address this issue by describing model bias in a Bayesian framework. The bias becomes an autoregressive term additional to white measurement noise, the only error type accounted for in traditional uncertainty analysis. To allow for bigger discrepancies during wet weather, we make the variance of bias dependent on the input (rainfall) or/and output (runoff) of the system. Specifically, we present a structured approach to select, among five variants, the optimal bias description for a given urban or natural case study. We tested the methodology in a small monitored stormwater system described with a parsimonious model. Our results clearly show that flow simulations are much more reliable when bias is accounted for than when it is neglected. Furthermore, our probabilistic predictions can discriminate between three uncertainty contributions: parametric uncertainty, bias, and measurement errors. In our case study, the best performing bias description is the output-dependent bias using a log-sinh transformation of data and model results. The limitations of the framework presented are some ambiguity due to the subjective choice of priors for bias parameters and its inability to address the causes of model discrepancies. Further research should focus on quantifying and reducing the causes of bias by improving the model structure and propagating input uncertainty.