The objectives of this work are to model spatially resolved passenger locomotive fuel use and emission rates, locate emissions hotspots, and identify strategies to reduce trip train fuel use and emissions. Train fuel use and emission rates, speed, acceleration, track grade, and track curvature were quantified based on over-the-rail measurements, using portable emission measurement systems, for diesel and biodiesel passenger rail service on the Amtrak-operated Piedmont route. Measurements included 66 one-way trips and 12 combinations of locomotives, consists, and fuels. A locomotive power demand (LPD) based emissions model was developed based on the physics of resistive forces opposing train motion, taking into account factors such as speed, acceleration, track grade, and curvature. The model was applied to locate spatially-resolved locomotive emissions hotspots on a passenger rail route, and also identify train speed trajectories with low trip fuel use and emissions. Results show that acceleration, grade, and drag are the major resistive forces affecting LPD. Hotspot track segments have 3 to 10 times higher emission rates than non-hotspot segments. Real-world trajectories are identified that reduce trip fuel use and emissions by 13 % to 49 % compared to the average. Strategies for reducing trip fuel use and emissions include dispatching energy-efficient and low-emitting locomotives, using a 20 % blend of biodiesel, and operating on low-LPD trajectories. Implementing these strategies will not only decrease trip fuel use and emissions but reduce the number and intensity of hotspots and, thus, lowering the potential for exposure to train-generated pollution near railroad tracks. This work provides insights on reducing railroad energy use and emissions, which would lead to a more sustainable and environmental-friendly rail transportation system.