Abstract: Because of climate change, the erection of dams through transboundary rivers, and the shortage of water resources, countries worldwide are facing several challenges. Unconventional water resources such as recycling wastewater are urgently needed to overcome the demand supply gap. The bioreactor is considered an effective means of removing contaminants and enhancing the self-purification of open waterways. This study numerically investigates the hydraulic impacts of an installed bioreactor in an open channel. Three-dimensional numerical models were developed based on computational fluid dynamics (CFD) to simulate different arrangements of the gravel bioreactor installed in the open channel. The relative heading up increased as Froude’s number increased, regardless of the number of bio-filter segments. The heading-up values decreased significantly when dividing the bio-filter into several segments with the same total length. The relative heading up decreased linearly as the distance between the bio-filter segments increased for a constant bio-filter length. On the other hand, the relative heading up increased linearly as the length of the bio-filter segments increased for a constant inter-distance of the bio-filter segments. For simultaneous changes in both the length of the bio-filter segments and their inter-distance, the relative heading up increased nonlinearly with the product of both the length and inter-distance. This study confirmed that the greater the inclination angles of the bio-filter’s face, the greater the heading up. When considering the base case with the inclination angle of 45, the increasing ratios of the relative heading up were 14.5%, 16.1%, and 19.7%, corresponding to the angles 60, 75, and 90, respectively.