Recent studies have demonstrated that positron emission tomography (PET) is a valuable tool for in-situ characterization of fluid transport in porous and fractured geologic media at the laboratory scale. While PET imaging is routinely used for clinical cancer diagnosis and preclinical medical research—and therefore imaging facilities are available at most research institutes—widespread adoption for applications in water resources and subsurface energy resources engineering have been limited by real and perceived challenges of working with this technique. In this study we discuss and address these challenges, and provide detailed analysis highlighting how positron emission tomography can complement and improve laboratory characterization of different subsurface fluid transport problems. The physics of PET are reviewed to provide a fundamental understanding of the sources of noise, resolution limits, and safety considerations. We then layout the methodology required to perform laboratory experiments imaged with PET, including a new protocol for radioactivity dosing optimization for imaging in geologic materials. Signal-to-noise and sensitivity analysis comparisons between PET and clinical X-ray computed tomography are performed to highlight how PET data can complement more traditional characterization methods, particularly for solute transport problems. Finally, prior work is critically reviewed and discussed to provide a better understanding of the strengths and weakness of PET and how to best utilize PET-derived data for future studies.