Although the deflector structures used in many fish habitat rehabilitation schemes are frequently overtopped, few studies have examined the scour patterns created around submerged models. Furthermore, laboratory studies typically test smooth-surfaced structures, when those installed in natural rivers are generally made of logs or boulders. This study uses rough-surfaced, paired deflectors to investigate the temporal evolution of scour for three overtopping ratios in identical approach flow conditions in a flume. Results show that when maintaining identical discharge, raising deflector height and thus reducing the overtopping ratio (flow depth / structure height), an increased depth and volume of scour is generated next to the structures. The location of maximum depth and the rate of scouring with time is similar for the two highest deflectors (overtopping ratios of 1.22 and 1.83), but different for the lowest deflector model (overtopping ratio of 3.67). In order to improve the success rate of river restoration projects using in-stream structures, the overtopping ratio should be used in equations that predict scour depth evolution with time.