An innovative approach to control scouring by stabilizing bed sediments using slag-based alkali-activated cement is presented. This method is economical, environmentally friendly, and easily implementable. Many experiments were conducted with various percentages of granular-ground-blast-furnace-slag (GGBFS). Results demonstrated that activated GGBFS is very efficient in stabilizing the bed sediment. For example, 9 wt.% GGBFS activated by 12.5 wt.% sodium hydroxide alkaline with a concentration of two molarities, after 7 days of curing, led to 110 times increase in critical shear stress of the stream bed. Furthermore, unconfined compressive strength tests were performed, revealing a linear relationship between the critical shear stress of treated bed sediments and their unconfined compressive strength. Additionally, the permeability of treated bed sediments was measured and was near the original granular sediments. Microstructure analysis experiments such as x-ray diffraction analysis, microscopic imaging, and scanning electron microscopy showed that the dominant product shaping the treated sediments is the calcium-aluminum-silicate-hydrate gel produced by the slag-based alkaline-activated cement.