The poor performance of critical zones along a railway line has long been a subject of concern for rail infrastructure managers. The rapid deterioration of track geometry in these zones is primarily ascribed to limited understanding of the underlying mechanism and scarcity of adequate tools to assess the severity of the potential issue. Therefore, a comprehensive evaluation of their behaviour is paramount to improve the design and ensure adequate service quality. With this objective, a novel methodology is introduced, which can predict the differential plastic deformations at the critical zones and assess the suitability of different countermeasures in improving the track performance. The proposed technique employs a three-dimensional geotechnical rheological track model that considers varied support conditions of the critical zone. The approach is successfully validated with published field data and predictions from finite element analysis. This methodology is then applied to a bridge-open track transition zone, where it is observed that an increase in axle load exacerbates the track geometry degradation problem. The results show that the performance of critical zones with weak subgrade can be improved by increasing the granular layer thickness. Interpretation of the predicted differential settlement for different countermeasures exemplifies the practical significance of the proposed methodology.