Improved understanding of microbe-water-subsurface porous media interactions that control biogeochemistry in subsurface aquifer and reservoir systems is critical from the perspective of a number environmental issues, such as Geological carbon sequestration, Bioremediation of Groundwater systems, and Energy resources recovery from subsurface. My approach involves using 2D microfluidic experimental test bed, usually called micromodels, to simulate subsurface hydrodynamic environment that allows in-situ visualization, tracking and quantification of biogeochemical reactions in subsurface reservoir systems. Several examples from reservoirs systems including bio-mineralization of CaCO3 during reactive transport in porous media its impact on pore space alteration and process efficacy and contaminants’ mixing enhancement during bacterial random motility will be discussed. A novel design of 2D- microfluidic experimental flow bed, based on real geo-materials as opposed to engineered materials in traditional micromodels, will be discussed. Finally, chemical imaging (Raman and Infrared spectroscopy) methods will be discussed for in-situ characterization of biogeochemical reactions in the flow cells as well as alternate analytical techniques in environmental engineering.