This article analyzes the spatio-temporal effect of the 2013 floods on freight traffic in Germany by using automatic traffic counter data. The methodology uses a proven time-series outlier detection and identification technique to endogenously determine if a counter was affected during the flood and estimate the magnitude and duration of the change in the number of vehicles passing through it. This is the first paper able to quantify climate-related variations in traffic across all the counters of a national network. Results show variations on 10% of all counters and 23% of all main roads. Results allow us to trace the configuration of disrupted and detour routes, recovery times, and the total effect on the network. Our findings serve as an input to other studies on the impact of exogenous events on the transport system and contribute towards the formulation of public policies to improve road resilience.