This research investigates the effect of heavy rain on highway traffic volume and average speed, and proposes a recharging well harvesting system as an alternative freshwater source in the context of climate change. The Cairo Autostorad highway was taken as a case study. The highway climate data were collected, and traffic was measured using Metrocount equipment during the period from 2008 to 2020. The results show that the studied road is about 12 km long, and about 40 water ponds exist along the route. Each pond has an estimated water volume of 300 m3, and a 30 cm recharging well, with a maximum recharging capacity of 25 m3/h with satisfactory performance, is recommended to be constructed for rainwater harvesting. The recharging wells will clear the ponding volume within 2.5 to 3.5 h after the rainfall has stopped. The design incorporates a 1.2 safety factor against blockage inside the well. In addition, a model was established between the average rainfall depth and the average measured highway speed for the period (2008–2020) during rainy months, indicating an exponential function with a determination factor R2 = 0.7076. The present rainfall (2020) and the representative concentration path (RCP) for 4.5 and 8.5 emissions scenarios were used to simulate the rainfall for future years: the 2040s, 2060s, 2080s, and 2100s. The results show that in the winter season for the current scenario (2020), the average rainfall depth was 45 mm, and the highway speed was 78 km/h. For the RCP 4.5 emission scenarios for the 2040s, 2060s, 2080s, and 2100s, the rainfall depths were 67.8, 126.4, 131.2, and 143.9 mm, and the corresponding reductions in the highway speeds were 23, 34, 35.3, and 36.9%, respectively, compared to the baseline scenario (2020). On the other hand, the RCP 8.5 emission scenarios show a reduction in the highway speed of 23, 34.5, 36.9, and 36.9% for the years 2040, 2060, 2080, and 2100, respectively, due to rainfall depths of 68.7, 128.4, 143.9, and 143.9 mm, respectively. This study helps policymakers to make wise decisions regarding sustainable water resource management and highway traffic problems related to rainwater depths in the context of climate change.