The deterioration of bridge substructure is a serious concern across the United States. The pier encasement is one of the most common practices for repairing and strengthening the bridge substructure. It is a rehabilitation process of existing pile piers during the repair or replacement of the bridge superstructure, which involves enclosing part of an existing pile pier with a polyethylene or PVC pipe large enough to provide at least three inches of concrete cover over the existing pier when filled. However, this process of enclosing pile piers might elevate water level due to increase in pier width, which could be hazardous in high-risk flood zones. Furthermore, it may create an adverse impact on the stability of the bridge due to scouring around the pier foundation. In order to gain knowledge on the backwater effect due to pile encasement, Hydraulic Engineering Center-River Analysis System (HEC-RAS) was used in this research to perform hydraulic simulations near the bridge sites. These simulations were carried out for various channel configurations and pier sizes with a wide range of flows, which resulted into 224 HEC-RAS models in order to investigate the effects of pile pier encasement on the headwater elevation. This study demonstrated that the water elevation measured in the upstream of the bridge showed no-rise condition, especially for wider channel sections with flatter slopes. However, the water elevation at the immediate upstream of the bridge was slightly higher, and the increasing pattern was only noticeable for a smaller channel width (20 ft), and specifically, for increased flow rate. As the area of flow was decreased resulting in increased water surface elevation due to encasement, a generic power equation in the form of Y = aXb was suggested for various channel slopes for the increased water surface elevation (Y) for each percentage decrease in channel area (X).