Flood scour is one of the major causes of bridge failures in the United States. Flood fragility curves can be used as an objective tool to assess the risk of a bridge to exceed some limit-states for a given flood. Despite the method's extensive use in seismic reliability analysis for civil infrastructures, the approach has rarely been utilized in evaluation of scour critical bridges. Flood fragility analysis of a instream bridge structure has been analyzed using first order reliability method. A MATLAB-based code has been developed to perform the analysis combining the first order reliability analysis tool of FERUM (Finite Element Reliability Analysis using MATLAB) and finite element structural analysis code ABAQUS. The developed code passes information back and forth between FERUM and ABAQUS in the iterative process to progress the analysis. Moreover, the code is capable of simulating scour depth, corresponding change in foundation parameter, variable limit-state for given inputs, which are realized by generating new finite element structural model each time FERUM calls ABAQUS. The proposed automated procedure has been demonstrated by deriving fragility curves, due to flood induced scour and stream water pressure, for a real bridge.