The present study proposes a method for evaluating the effectiveness of road‐crossing drainage culverts in ephemeral streams. This approach is focused on estimating the culvert capacity in road–stream crossings and the probable runoff generated on the road from hydrological thresholds associated with hydromorphological criteria. In particular, discharges at bankfull and flood‐prone stages have been used in combination with 2.5 and 100‐year peak discharges. Different hydraulic variables have been considered for calculating the discharge through culverts under these conditions (e.g. tailwater and headwater depth, inlet control, pipe roughness, pipe cross‐area and slope, pipe outlet velocity, critical water depth, and flow rate over the road). Geomorphological factors such as bed stability, bed load transport, and channel roughness have also been considered because of their potential for obstructing the drains in this type of channel. In addition, a potential obstruction index (PIOBSTR) has been calculated, as a dependent parameter of the obstacle index (IOBST) and the potential build‐up of coarse sediments (PBCS). The study has been carried out on the Mediterranean coast in the region of Murcia (Spain), where there are numerous examples of road–stream crossings equipped with culverts in ephemeral channels that could cause highly dangerous situations for road traffic. Copyright © 2012 John Wiley & Sons, Ltd.