Interaction of aqueous fluids with the rock matrix within which they reside can yield a variety of phenomena due to the coupling of reaction transport and mechanical processes; many of these have potentially important implications for exploration and exploitation of energy and mineral resources. We investigated effects of nucleation to produce banded precipitation; Darcy-mineral dissolution coupling to produce scalloped, fingered and more complex alteration front morphologies, and diagenetic alteration in chemically complex, multi-mineralic systems. Migration of methane driven by buoyancy effects was shown to lead to cellular and temporally oscillatory flows. Sandstones at depth experiencing pressure solution display unstable compaction leading to formation of stylolites and band-like regions of augmented compaction alternating with low porosity bands with augmented overgrowth. It was shown that transfer of natural gas from shale source rock into neighboring sandstones could occur through a series of discrete pulsatile events through a cycle of fracturing and healing.