To study the hyporheic exchange driven by a single peak flood-induced water level fluctuation (i.e. flood wave), a method combining numerical simulation with theoretical derivation was proposed based on the Inbuk Stream, Korea, where flooding occurs frequently. The hyporheic exchanges induced by different flood waves were investigated by varying amplitude (A), duration (T), wave type parameter (r), and rising duration (tp), which were adopted from the real-time stream stage fluctuations. Additionally, the idea of constant upstream flood volume (CUFV) condition for flood waves was put forward, and the effects of “Botan” (T/A) and peak number (N) on hyporheic exchange were studied. The results showed that the hyporheic exchange flux (q) was controlled by the water level h (sine-type) and its change rate v (cosine-type), and was proportional to the polynomial of them q“∝” (ω∙h+v), where ω is the angular frequency of the flood wave. Based on this mechanism, the influence principles on hyporheic exchanges of the typical flood wave parameters (A, T, r and tp) as well as T/A and N under CUFV condition were clarified. The main characteristic variables of hyporheic exchange, which were maximum aquifer storage and residence time, were positively correlated. They also had positive relations to the integral of the flood wave over time, which increased when the wave became higher, wider, rounder and less skewed. However, when CUFV condition was imposed, the residence time was positively correlated with T/A, whereas the maximum aquifer storage was negatively correlated with T/A. With the increase in N, water exchanged more frequently and some water returned to the stream early, leading to the slight decrease in maximum aquifer storage and residence time. These findings enriched the theory of hyporheic exchange driven by surface water fluctuation and be of great significance to enhance pollutant degradation in the hyporheic zone downstream of reservoirs.