Distribution of the water flow path and residence time (HRT) in the hyporheic zone is a pivotal aspect in anatomizing the transport of environmental contaminants and the metabolic rates at the groundwater and surface water interface in fluvial habitats. Due to high variability in material distribution and composition in streambed and subsurface media, a pragmatic model setup in the laboratory is strenuous. Moreover, investigation of an individual streamline cannot be efficiently executed in laboratory experiments. However, an automated generation of water flow paths, i.e., streamlines in the hyporheic zone with a range of different streambed configurations could lead to a greater insight into the behavior of hyporheic water flow. An automated approach to quantifying the water flow in hyporheic zone is developed in this study where the surface water modeling tool, HER-RAS, and subsurface water flow modelling code, MIN3P, are coupled. A 1m long stream with constant water surface elevation of 2 cm to generate hydraulic head gradients and a saturated subsurface computational space with the dimensions of x:y:z = 1:0.1:0.1 m is considered to analyze the hyporheic exchange. Response in the hyporheic streamlines and residence time due to small-scale changes in the gravel-sand streambed were analyzed. The outcomes of the model show that the size, shape, and distribution of the gravel and sand portions have a significant influence on the hyporheic flow path and HRT. A high number and length of the hyporheic flow path are found in case of the highly elevated portion of gravel pieces. With the increase in the base width of gravel pieces, the length of hyporheic flow path and HRT decreases. In the case of increased amounts of gravel and sand portions on the streambed, both the quantity and length of the hyporheic flow path are reduced significantly.