We investigate the potential for improved recovery of subsurface energy resources (hydrocarbons or heat) through in-depth diversion technology. A number of pilot studies in the North Sea have demonstrated in recent years that sodium silicate can be used to block preferential flow paths and divert water to previously unswept areas of a reservoir. Accompanying simulation studies based on an explicit weak coupling of a reservoir flow simulator and an external chemical module have attempted to replicate the observed behaviour. Since the development of silicate gels and the accompanying permeability reduction is essentially a coupled flow-chemical process, we first will present a fully implicit compositional-reactive flow and transport implementation and investigate the impact of the grid and time-stepping resolution on simulation performance in 2D subsurface reservoirs mimicking petroleum and geothermal applications. We proceed to investigate the sensitivity of the recovery to design parameters of the in-depth diversion strategy. Since adjoint gradients are not typically available for these parameters and uncertainties associated with an application of in-depth divergence are large, we use an ensemble-based methodology to perform an optimization study. This study aims to find optimal strategies for combined waterflooding and design of in-depth diversion under geological uncertainty. It is demonstrated that in-depth diversion can significantly extend the life-time of hydrocarbon or geothermal fields when the timing of injection and the size of the sodium silicate batch is optimized. Finally, we discuss methods that help to address an issue of computational cost associated with the high resolution required for accurate simulation of the coupled process.