Biodegradable prefabricated vertical drains (BPVD) made from naturally occurring materials such as jute and coconut (coir) fibre not only have favourable engineering characteristics but also not detri-mental to the natural environment thanks to their biodegradability. Although the use of these natural fibre drains has been proposed for several decades, their application is still very limited. One of major reasons for this is because they are usually composed of individual fibres with large openings which can trap fine soils while discharging pore pressure, consequently reducing the hydraulic conductivity of the drain. This study therefore aims to clarify how soil can clog and damage the porous nature and hydraulic properties of fibre drains through an experimental scheme. A typical natural fibre drain composed of a jute sheath and coconut core was adopted in this investigation. A series of discharge capacity tests, in which the drain was confined by soft clay, were conducted. The drain was then subjected to a post-analysis process using micro-CT scanning to identify how the fine soil has penetrated into the drain and whether this has degraded the discharge capacity of the drain. The results indicate that the current drains can resist well soil clogging due to an initial confining pressure of 50 kPa but the drain discharge capacity can decrease considerably if a higher initial confining pressure, i.e., 100 kPa, is applied.