Tropical forests comprise 40% of the Earth’s terrestrial carbon sink, converting carbon dioxide into biomass. The natural flux of carbon in forests is controlled by growth and decomposition of biomass; processes which can be influenced by human activity. Southeast Asia’s history of intensive commercial logging has interrupted these natural processes, with 70% of extant forests now degraded. Despite their prevalence, logged forests are not studied as widely as primary forests. Data on belowground biomass and root systems is particularly scarce. Malaysian Borneo has been a global hotspot for timber production over the past century, often at greater rates than were considered sustainable. This casts doubt on whether heavily degraded forests will regenerate naturally within the expected timeframe of approximately 60-80 years. This thesis aims to fill these knowledge gaps by investigating the above and belowground biomass of Bornean forests along a degradation gradient, from highly degraded salvage-logged forests, to lightly logged forest, through to pristine primary forests. First, we trialled LiDAR and photogrammetry for generating 3D imagery of tree root systems using low-cost, handheld technology. We then used this technique to digitally capture the root system architecture of Macaranga trees excavated in Borneo and determined the biomass root:shoot ratio. Finally, we used data from an eight-year vegetation census across the degradation gradient to parameterise a simulation of biomass regeneration in logged forests. We found that the pioneer species in regenerating forests have a higher root:shoot ratio than is found in a primary forest and that Macaranga tree roots form complex networks by inosculating with their neighbours. Our simulation indicates that by 2050, most salvage-logged forests will remain degraded. We also showed that primary forests can continue to gain large amounts of biomass year-on-year. The outputs from this research can support restoration activities, advise sustainable logging, and improve local carbon accounting.