Measuring the bridge frequencies indirectly from an instrumented test vehicle is a potentially powerful technique for its mobility and economy, compared with the conventional direct technique that requires vibration sensors to be installed on the bridge. However, road surface roughness may pollute the vehicle spectrum and render the bridge frequencies unidentifiable. The objective of this paper is to study such an effect. First, a numerical simulation is conducted using the vehicle-bridge interaction element to demonstrate how the surface roughness affects the vehicle response. Then, an approximate theory in closed form is presented, for physically interpreting the role and range of influence of surface roughness on the identification of bridge frequencies. The latter is then expanded to include the action of an accompanying vehicle. Finally, measures are proposed for reducing the roughness effect, while enhancing the identifiability of bridge frequencies from the passing vehicle response.