Each fuel cell component of a proton exchange membrane fuel cell (PEMFC) used in automotive application operates most effectively (from performance and durability standpoints) within specific ranges of water content and temperature. The water and heat transport processes are coupled and present a challenge in providing the right balance over the entire range of operating conditions. Another important related aspect is CO poisoning of the electrocatalyst, which adversely affects the fuel cell performance. Freezing and cold-start present additional challenges for automotive PEMFCs. A critical review of the recent developments on these topics is presented in this paper. The study covers both the microscopic and macroscopic aspects of the transport within membrane, catalyst layers, gas diffusion layers, and gas channels, and an overview of the current PEMFC cooling technology. After discussing the current status, suggestions for future work on the above topics are presented.