Deep subsurface stimulation processes often promote fluid-rock interactions that can lead to the formation of small colloidal particles that are suspected to migrate through the rock matrix, partially or fully clog pores and microfractures, and promote the mobilization of contaminants. Thus, the goal of this work is to understand the geochemical changes of the host rock in response to reservoir stimulation that promote the formation and migration of colloids. Two different carbonate-rich shales were exposed to different solution pHs (pH = 2 and 7). Iron and other mineral transformations at the shale-fluid interface were first characterized by synchrotron-based XRF mapping. Then, colloids that were able to migrate from the shale into the bulk fluid were characterized by synchrotron-based extended X-ray absorption structure (EXAFS), scanning electron microscopy (SEM), and single-particle inductively coupled plasma time-of-flight mass spectrometry (sp-icpTOF-MS). When exposed to the pH = 2 solution, extensive mineral dissolution and secondary precipitation was observed; iron-(oxyhydr)oxide colloids colocated with silicates were observed by SEM at the fluid-shale interfaces, and the mobilization of chromium and nickel with these iron colloids into the bulk fluid was detected by sp-icpTOF-MS. Iron EXAFS spectra of the solution at the shale-fluid interface suggests the rapid (within minutes) formation of ferrihydrite-like nanoparticles. Thus, we demonstrate that the pH neutralization promotes the mobilization of existing silicate minerals and the rapid formation of new iron colloids. These Fe colloids have the potential to migrate through the shale matrix and mobilize other heavy metals (such as Cr and Ni, in this study) and impacting groundwater quality, as well produced waters from these hydraulic fracturing operations.