Low-permeability aquitards can significantly affect the transport, distribution, and persistence of contaminant plumes in subsurface systems. Although such low-permeability materials are often charged, the key role of charge-induced electrostatic processes during contaminant transport has not been extensively studied. This work presents a detailed investigation exploring the coupled effects of heterogeneous distribution of physical, chemical and electrostatic properties on reactive contaminant transport in field-scale groundwater systems including spatially distributed clay zones. We performed an extensive series of numerical experiments in three distinct heterogeneous sandy-clayey domains with different levels of complexity. The flow and reactive transport simulations were performed by explicitly resolving the complex velocity fields, the small-scale electrostatic processes, the compound-specific diffusive/dispersive fluxes and the chemical processes utilizing a multi-continua based reactive transport code (MMIT-Clay). In each particular domain, numerical experiments were performed focusing on both the forward and back diffusion through the sandy-clayey interfaces. The results illuminate the control of microscopic electrostatic mechanisms on macroscopic mass transfer. Coulombic interactions in the clay's diffuse layer can significantly accelerate or retard a particular species depending on its charge. Furthermore, the chemical heterogeneity plays a major role in mass storage and release during reactive transport. Neglecting such processes can lead to substantial over- or underestimation of the overall transport behavior, which underlines the need for integrated physical, chemical and electrostatic approaches to accurately describe mass transfer processes in systems including low-permeability inclusions.