The devised transport of a mobile phase and complex sample mixtures through high and low surface area materials induced by an externally applied electrical field plays a central role in analytical, technological, and environmental processes, including the dewatering of waste sludge and soil remediation, capillary electrophoresis, or electrochromatographic separations in particulate and monolithic fixed beds, as well as micro-chip devices. Transport is primarily achieved via electromigration of ions (background electrolyte), electrophoresis (charged analyte molecules or particles), and electroosmosis (bulk liquid) driven by the shear stress concentrated in the electrical double layer (EDL) at charged solid-liquid interfaces. The local and macroscopic behaviour and long-time average magnitude, stability, and uniformity of electroosmotic flow (EOF) in porous media are related to the physicochemical nature of the surface, the pore space morphology, and properties of the liquid electrolyte. A detailed analysis of these parameters has a fundamental importance as it guides performance and design strategies of an electrokinetic process with respect to diffusive-convective transport schemes. This immediately addresses fundamental aspects of capillary electrochromatography (CEC) as a rapidly emerging technique, which was proposed to add a new dimension to separation science. Bulk hydrodynamic flow is achieved by electroosmosis, employing stationary phases usually developed for liquid chromatography (LC). In a very simple way CEC is often described as a hybrid technique between capillary zone electrophoresis (CZE) and LC. From an analytical point of view CEC has not yet overcome its typical “infancy problems”, even though one can recognize an increasing number of applications. The reasons are found in relatively early anticipations, regarding EOF velocity profile through more complex porous media (usually borrowed from an open tube as in CZE) and theoretical assumptions for achieving differential migration (by simply synthesizing retention by chromatographic and electrophoretic formalism). In this thesis the most fundamental aspects of capillary electrochromatography (CEC) are addressed. It is shown that CEC is far more complex than may be anticipated from the two components involved in this method. The first one is CZE, which (as an electrokinetic separation method) appears to be almost under control, because of its increasing number of applications in the pharmaceutical industry. The second one is LC, which is the strongest working horse for almost all analytical separation problems at hand and has no competitor in view of reliability and robustness. In this line it will keep its strong role among analytical separation techniques. The most important implementations for CEC are an increase of the complexity of phenomena involved in the mobile phase transport through a hierarchical porous medium (“Flow aspects”) and also “Transport aspects” of charged analytes. These phenomena have been systematically addressed in the present thesis and made quantitatively acessible. The unique combination of quantitative optical imaging techniques and chromatographic field studies revealed a quantitative orthogonal view on the investigated flow aspects in electrochromatographic separation systems. The investigated phenomena are highlighted and are successfully employed for separations in the pharmaceutical and bio-analytical field, being more important for resolving the relevant transport aspects of analytical target molecules in hierarchically structured porous media.