Transition zones in railway tracks are the locations with considerable changes in vertical support structures, e.g., near bridges. Due to possible water flow constrictions in transition zone structures, there is frequently an increased moisture level in the ballast/subballast layers, which is a potential source of track degradation. This paper presents results of the moisture condition measured in three transition zones using ground penetrating radar, where the ballast/subballast are analyzed. The relationship between the moisture condition and track degradation in the transition zones is studied by comparing it to the longitudinal track level that is measured by the track inspection coaches. A strong connection is found between the high moisture condition and track degradation in the transition zones. The dynamic behavior of the transition zones with high moisture condition is analyzed using the Finite Element method. Differential stiffness and settlement are taken into consideration in the transition zone model, which is also coupled with a vehicle. The ballast/subballast layers are modelled as solid elements. Increased moisture conditions are considered as a reduction of elastic modulus, according to laboratory findings. Results show that high moisture leads to an increase of dynamic wheel loads in the transition zone, which explains the connection and confirms that the high moisture condition is a source of transition zone problems.