Flood and stream induced scour occurring in bridge piers located on rivers is one of the mostly observed failure reasons in bridges. Scour induced failure risk in bridges and determination of the alterations in bridge safety under seismic effects has the ultimate importance. Thus, for the determination of bridge safety under the scour effects, the scour amount under bridge piers should be designated realistically and updated with continuous monitoring. In this study, in order to measure the amount of scour in bridge piers unmanned aerial system (UAS) based measurement methods were implemented. UAS based measurement systems provide new and practical approach and bring high precision and reliable solutions considering recent measurement systems. For this purpose, the reinforced concrete (RC) bridge that is located on Antalya Bogacayi River, Turkey and that failed in 2003 due to flood-induced scour was selected as the case study. The amount of scour occurred in bridge piers was determined realistically, and the behavior of bridge under scour effects was investigated. In the light of the attained scour measurements and expected scour after a probable flood event, the behavior of scour induced RC bridge was determined by pushover analyses under seismic loadings. In the analyses, the load and displacement capacity of bridge was observed to diminish significantly under expected scour. Regarding the case study, UAS based and continuously updated bridge performance evaluation system was developed that could be used for bridges located on the riverbed.