Proton Exchange Membrane Fuel Cells (PEMFCs) are known as a promising alternative for internal combustion engines (ICE) to reduce pollution. Recent progress of PEMFCs is heading towards achieving higher power densities, reducing the refueling time, and decreasing the degradations, to facilitate the commercialization of hydrogen mobility. Model-assisted stack component development, diagnosis, and management are essential to ensure improved stack design and operation for tackling the existing implementation challenges of PEMFCs. Past reviews usually touched on a specific aspect, which can hardly provide the readers a complete picture of the key challenges and advances in water management. This paper aims at delivering a comprehensive source to review, from both experimental, analytical, and numerical viewpoints, the key operational challenges, and solutions of the stack to improve water/thermal management and cold start. In addition to presenting the fundamental theory to develop an analytical model, the recent advances in the flow field design, nanofluid coolants, and cold-start methods. Furthermore, the impacts of microstructural properties and the design of the porous layers on the water/thermal management are described.