The change of vertical hydraulic conductivity (K v) before and after a flood season is crucial in understanding the long-term temporal variation of streambed permeability. Therefore, in this study, a detailed K v field investigation was conducted at an in-channel site within the Dawen River, China, before and after a flood season. In-situ falling-head permeameter tests were performed for the determination of K v. The tests were conducted using a 10 × 10 grid, at five different depths. In total, 871 valid K v values from layers 1–5 were obtained. The Kruskal-Wallis test on these K v values before and after the flood season shows they belonged to different populations. The sediments before the flood season primarily consisted of sand and gravel, whereas after the flood season, patchy distribution of silt/clay occurred in the sandy streambed and silt/clay content increased with the increasing depth; under the losing condition during flooding, downward movement of water brought fine particles into the coarse sediments, partially silting the pores. Accordingly, the K v values after the flood season had a smaller mean and median, and a higher level of heterogeneity, compared to those before the flood season. Additionally, the distribution pattern in K v across the stream differed before and after flood season; after the flood season, there was an increasing trend in K v from the south bank to the north bank. Overall, the contrasts of K v before and after the flood season were predominantly subject to the infiltration of fine particles.