Flow channelization originates from the inherent structural complexity of geologic materials and has an enormous influence on engineering endeavors, including groundwater management and remediation, geologic carbon storage, and geotechnical engineering. The research presented herein improved our understanding of the inherently complex structures that underpin flow and transport processes in groundwater systems and developed models capable of capturing those complexities. The work integrated novel graph theory and optimization techniques to improve our understanding of (1) the relationship between structure and flow distribution, (2) the impact of flow heterogeneity on a reaction's spatial distribution, and (3) the evolution of flow and transport under uniform erosion. The findings are directly translatable to flow, transport, and reaction modeling. Chapter 1 presents background information, describes state-of-the-art methodology for the field, and identifies current research needs. The following three chapters present the completed research, which addresses the noted knowledge gaps concerning flow in heterogeneous porous media. Chapter 2, Flow Path Resistance in Heterogeneous Porous Media Recast Into a Graph-Theory Problem, had two primary goals. First, to devise an efficient graph-based representation of flow development in porous media that identified the paths of least resistance from structural attributes alone. Second, to elucidate the structural constraints that arrange flow into preferential paths and stagnation zones at the pore scale. In achieving those goals, we developed a quantitative assessment of flow channeling, successfully predicted the spatial distribution of fast flow paths from structural data alone, and found that the local structure order dictates flow partitioning into preferential and stagnant regions. Chapter 3, Flow Heterogeneity Controls Dissolution Reaction Behavior in Geologic Porous Media, quantified how flow heterogeneity causes non-uniformly spatially distributed reactions. The work yielded a revised dissolution behavior diagram and effective reaction rate model that correctly predicted the dissolution patterns and observed reaction rates using known flow, transport, and reaction properties. Chapter 4, titled Evolution of Flow and Transport under Uniform Erosion, aimed to better understand the implications of flow and transport when a pore space's geometry changes while the topology is constant. We found that microscopic, uniform changes to the pore structure geometry have strong implications for macroscopic structural connectivity, flow distribution and transport behavior, and the structural topological order. In addition, we demonstrated that the initial structural heterogeneity dictates the evolution of flow and transport behavior from uniform/Fickian to channelized/anomalous and vice versa. We conclude this dissertation in Chapter 5 with a summary of the significant outcomes from the research projects and a discussion on the implications for modeling flow and transport processes in porous media at the pore scale.