The hyporheic zone (HZ) is the area where surface water and groundwater interact in sediments immediately beneath and adjacent to streams, rivers, and riverine estuaries. It possesses unique chemical and biological properties stemming from the mixing between groundwater and surface water (Hester & Gooseff, 2010), and its high potential for nutrients removal and pollutant attenuation has attracted the attention of many researchers (Galloway et al., 2019). The hyporheic flow (Q h) is hydrologically defined as the volume of stream water per unit of time, which flows through the subsurface domain, and it starts and terminates at the stream after a certain period of time (Gooseff, 2010). The hyporheic flux (q h) is the corresponding flow per unit area through the streambed. It differs from groundwater flux by its exchanging back and forth across the sediment-water interface (SWI) at a relatively small scale, typically centimeters to tens of meters; however, groundwater flow travels unidirectionally over much longer distances (Boano et al., 2014). Geomorphic features, including alternate bars, ripples, and meanders, can play a significant role in hyporheic flow characteristics (Herzog et al., 2016). A distinctive feature of alternate bars emerges from the induced 3-D patterns of hyporheic flow due to the hydraulic head variation on its morphology (Tonina & Buffington, 2007, 2009; Trauth et al., 2013). Many studies have been carried out on the HZ characteristics in the 3-D gravel bars morphology. Laboratory experiments and 3-D dimensional modeling were conducted to investigate the effect of streamflow and bar's amplitude variations on hyporheic exchange (Tonina & Buffington, 2007). Besides, the alluvium depth can constrain the HZ extent (Tonina & Buffington, 2011). A predictive model was proposed to estimate the hyporheic residence times (T) dependence on bar submergence, hydraulic conductivity, and the slope of a stream reach (Marzadri et al., 2010). Moreover, the undermining effect of ambient groundwater on HZ was analyzed by Trauth et al. (2013) for fully submerged bars. Despite these many studies, the HZ characteristics in partially submerged bars are not fully understood. The importance of bars with low submergence lies in their common occurrence during low stream flow periods,