Riffle-pool sequences are fundamental, ubiquitous morphological features of alluvial rivers that are thoroughly studied in general and commonly incorporated into river restoration projects. Most previous investigations on the effect of riffle-pool sequences on hyporheic exchanges focused on solely bed undulation, because that is widely thought to be the defining feature of riffle-pool sequences. However, riffle- pool sequences also have significant width undulations that are vital to riffle-pool sequences morphodynamics, yet relatively few studies exist on the effect of such undulations on hyporheic exchanges. Thus, in this study based on laboratory experiments and numerical simulations, we investigate the effect of bed and width undulations on hyporheic zone characteristics for various ratio of width amplitude to bed amplitude. The variation of hyporheic exchange characteristics (i.e. hyporheic exchange flux and residence time) for different riffle-pool designs were also assessed by creating prescribed topography of synthetic river valleys. The results showed that due to pressure variation along width undulations, the upwelling and downwelling patterns can also be observed for only width undulations in rivers, in the absence of bed undulations, and as width undulation amplitude decreases, the normalized hyporheic exchanges (Q*HZ) increase and normalized median residence time (RT*) decreases. Also, simultaneous channel bed and width undulations result in higher Q*HZ especially when a pool is located in an expansion (aka “oversized” cross-section) and a riffle in a constriction (“nozzle”). Our results suggest that river restoration project that artificially construct wide pools and constricted riffles will achieve maximum Q*HZ and RT*, though they will not be geomorphically self-sustainable.