Subsurface flow of multiphase, multicomponent fluids is complex and not well understood. Pore-scale phenomena dictate the overall behavior of the reservoir. The root of multiphase, multicomponent pore-scale dynamics lies in fluid-fluid and fluid-mineral interactions at the microscopic scale. Fundamental understanding of the pore-scale interactions between the various phases and components in subsurface formations is essential to optimize the design of subsurface energy and environmental resources. Management methods of subsurface resources, for example improved oil recovery and CO2 storage security, are assessed in terms of recovery effectiveness, economic benefit, and cost. These factors are all strewn with open questions in complex fluid transport through porous rock materials. To address questions of fluid-fluid and fluid-mineral interactions at the fundamental pore-level, microfluidics, or the study of fluids at the sub-millimeter scale, is well positioned to contribute improved understanding. Specifically, microfluidics lends a direct eye into the microscale world of porous materials. In this work, microfluidics with representative geometry, length scales, and, importantly, surface mineralogy, are developed and used to delineate the fundamental mechanisms dictating the pore scale fluid behavior of multiphase, reactive fluid transport through porous materials. Fundamental mechanisms dictating (i) low salinity waterflooding, a method to improve oil recovery with low economic and environmental costs; (ii) reactive transport, important to the assessment and design of geological CO2 storage security; and (iii) miscible fluid interactions, of industrial interest to heavy oil recovery are delineated in this work. The following describes each contribution briefly. First, low salinity waterflooding is a promising technique to increase oil recovery in an economic manner. The fundamental mechanisms that dictate this process, however, are poorly understood due to conflicting core flooding and field evidence. It has been suggested that the presence of clay significantly impacts pore wettability and low salinity oil recovery from sandstones. Direct visualization of the pore-scale dynamics during low salinity waterflooding is required to provide a mechanistic understanding of the low salinity effect. In this work, two-dimensional silicon microfluidic networks with representative pore geometry (i.e., micromodels) are modified to achieve the surface characteristics required for representative crude oil, brine, and rock interactions. Specifically, clay particles are deposited into the micromodel pore space to enable direct pore-scale, real-time visualization of fluid-solid interactions with representative pore-geometry and realistic surface interactions between the reservoir fluids and the formation rock. The surface functionalized micromodels are then used to determine the conditions at which stably adhered clay particles detach and to study the pore-level interactions between the crude oil, brine, and solid surfaces during aging and during low salinity brine injection. The experimental results provide a basis for improving the basic understanding of the mechanisms at play. Pore-scale flow simulation is used to corroborate experimental observations of the dominant mechanism(s) at play during low salinity waterflooding in sandstones. Mechanistic understanding of pore-level behavior sets the basis for upscaling and informing the design of optimal injection fluids at the field scale. Second, formation damage is observed during field-scale low salinity waterflooding due to fine clay particles mobilization. The overall effect on the pore-scale, and its impact on oil recovery, is not well understood. Using the clay-functionalized micromodel developed in this work, the mobilization of clay particles, its impact on flow paths, and its effect on oil recovery is investigated. Pressure measurements showed 6-fold reductions in permeability as a result of kaolinite migration and flow path blockage under low salinity conditions. Swelling of montmorillonite clay particles were observed at low salinities. Significantly, pores most susceptible to particle mobilization and flow path blockage are correlated inversely with improved oil recovery. Flow diversion due to preferential flow path blockage is proposed as a mechanism dictating improved oil recovery at low salinities. Third, evolution of pore-surface wettability, or, aging, and the interplay between clay minerals and the crude oil and brine remain an open question in creating initial subsurface reservoir conditions in the laboratory and in understanding the underlying mechanisms of the low salinity effect. The ability to recreate wetting and fluid-mineral conditions similar to realistic subsurface systems is central to the design of improved oil recovery methods. In this work, we provide direct observation of water-wet surfaces shift towards mixed-wettability due to attraction between charged clay particles and crude oil. Low salinity waterflooding of this aged system reveals a new Pickering emulsification mechanism by which preferential flow paths are obstructed, leading to flow diversion through oil-filled pores to improve overall oil recovery. Fourth, transport through carbonates is complicated by the reactive nature of the rock. Carbonates are reactive and highly susceptible to dissolution. Formation stimulation (i.e., acidizing) and CO2 storage involve the flow of acidic fluids through the carbonate pore space. Importantly, reactive flow alters both the surface properties of the pore space and the pore geometry. Dissolution and flow behavior at the pore scale must be understood to engineer effective formation stimulation and safe CO2 storage projects. In this work, calcite-functionalized microfluidic systems are developed and used to delineate the interplay between dissolution, flow, and surface wettability. Specifically, two-dimensional calcite-functionalized micromodels with representative pore geometry and surface properties are developed in this work to study the dissolution of carbonates under acidic flows. Significantly, a new mechanism is discovered whereby the reaction product, CO2, is wetted on the reactive grain surface and protects the grain from further dissolution. Experiments show similar effects at a range of temperatures, pressures, and acidities corresponding to surface and subsurface conditions. To further delineate the conditions required for the grain-engulfment effect to dominate, a polymer-based non-reactive microchannel containing an embedded reactive calcite post is developed. Flow regimes corresponding to the observed grain-engulfment mechanism in porous media were delineated using the one-dimensional reactive transport devices and provide a first order understanding for large-scale CO2 storage security assessments. Fifth, miscible fluid interactions underlie many physical processes in natural and engineered systems. Injection of solvents that are miscible with crude oil, or solvent-enhanced oil recovery, aims to improve heavy-oil recovery that tends to be highly viscous and immobile. This work investigates the interactions between the fluids under microconstrained geometries similar to geological porous media. Importantly, spontaneous fingering between the crude oil with complex composition and the solvent is observed. That is, fractal-like fingers are generated in the absence of an applied external pressure gradient, i.e., zero imposed Peclet number. The surprising dynamics observed are a result of the complex composition of the crude oil; light crude-oil components are mobile and are exchanged with the solvent phase while heavy crude-oil components are less so and remain. Recursive diffusion-driven mass exchange leads to local instabilities at the interface that result in differences in dynamic interfacial tension along the interface and leads to fractal-like fingering. The resulting Marangoni flow enhances the mass exchange until components in the crude oil phase reach local equilibrium with those in the solvent phase. The surface-functionalized devices developed in this work enables a wide range of investigations to the fundamental mechanisms dictating transport through subsurface systems. Importantly, the new fundamental mechanisms delineated in this work are of fundamental importance to the understanding and design subsurface energy and environmental resources management and to the broader field of engineering science.