Species transport in nanocapillary membrane systems has engaged considerable research interest, presenting technological challenges and opportunities, while exhibiting significant deviations from conventionally well understood bulk behavior in microfluidics. Nonlinear electrokinetic effects and surface charge of materials, along with geometric considerations, dominate the phenomena in structures with characteristic lengths below 100 nm. Consequently, these methods have enabled 3D micro- and nanofluidic hybrid systems with high-chemical selectivity for precise manipulation of mass-limited quantities of analytes. In this review, we present an overview of both fundamental developments and applications of these unique nanocapillary systems, identifying forces that govern ion and particle transport, and surveying applications in separation, sensing, mixing, and chemical reactions. All of these developments are oriented toward adding important functionality in micro-total analysis systems.