Current environmental and energy sustainability trends have instigated considerable interest in alternative energy technologies that exhibit reduced dependence on fossil fuels. The advantages of such a direction are two-fold: reduced greenhouse gas emissions (notably CO2) and improved energy sustainability. Fuel cells are recognized as a potential technology that achieves both of these goals. However, improvements to fuel cell power density and stability must be realized to make them economically competitive with traditional, fossil-based technologies. The work in this dissertation is largely focused on the use of analytical tools for the study of transport processes in three fuel cell systems toward improvement of fuel cell performance. Polymer electrolyte membrane fuel cells (PEMFCs) are fueled by hydrogen and oxygen to generate electrical current. Microbial fuel cells (MFCs) use bacteria to degrade carbon compounds, such as those found in wastewaters, and simultaneously generate an electric current. Enzyme fuel cells (EFCs) operate similarly to PEMFCs but replace precious metal catalysts, such as platinum, with biologically-derived enzymes. The use of enzymes also allows EFCs to utilize simple carbon compounds as fuel. The operation of all three fuel cell systems involves different modes of ion and electron transport and can be affected negatively by transport limitations. Electrochemical impedance spectroscopy (EIS) was used in this work to study the distribution of transport resistances in all three fuel cell systems. The results of EIS were used to better understand the transport resistances that limited fuel cell power output. By using this technique, experimental conditions (including operating conditions, construction, and materials) were identified to develop fuel cells with greater power output and longevity. In addition to EIS, neutron imaging was employed to quantify the distribution of water in PEMFCs and EFCs. Water content is an integral aspect of providing optimal power output from both fuel cell systems. Neutron imaging contributed to developing an explanation for the loss of water observed in an operating EFC despite conditions designed to mitigate water loss. The findings of this dissertation contribute to the improvement of fuel cell technology in an effort to make these energy devices more economically viable.