The consolidation and settlement of soft soil foundations pose significant challenges in geotechnical engineering, where prefabricated vertical drains (PVDs) are commonly used to accelerate consolidation. Accurate prediction of consolidation behaviour is influenced by several factors, including loading patterns, soil layering, and particularly drainage conditions. Traditional analytical and numerical methods often make oversimplified assumptions about drainage conditions, potentially leading to inaccuracies in predicting excess pore water pressure (EPWP) dissipation and settlement. This study presents a novel spectral-based approach for analysing the consolidation behaviour of PVD-assisted multilayered soils subjected to time-dependent loading and general drainage boundary conditions. By using matrix operations, the excess pore water pressure (EPWP) across different soil layers is expressed as a unified solution, which effectively captures the influence of varying drainage conditions. The proposed method is validated through comparisons with laboratory test, field data and some existing solutions, demonstrating improved accuracy and flexibility in predicting EPWP dissipation and settlement. The results highlight the potential overestimation of consolidation when traditional boundary assumptions are applied and underscore the importance of considering more general drainage boundaries, providing practical insights for engineering design and settlement prediction in PVD-assisted foundations.