Free-carrier absorption (FCA) has proven to be an important obstacle in the development of a silicon-based laser; however, FCA may serve as a potential advantage in active silicon-based switches or modulators. In this work, we present FCA modulation in slot waveguides with silicon nanocrystals (Si-ncs) embedded in ${\mathrm{SiO}}_2$ as the low-index slot material. Slot waveguides were fabricated with and without Si-ncs, and the presence of Si-ncs was shown to increase the pump-induced FCA loss in the waveguides by a factor of 4.5. We modeled the Si-nc material using a four-level rate equation analysis to estimate the excited population of Si-ncs, allowing us to extract a value of $2.6\times {10}^{-17}{\mathrm{cm}}^2$ for the FCA cross section of the Si-nc material.