Radionuclide extraction, processing and storage have resulted in a legacy of radionuclide-contaminated groundwater aquifers worldwide. An emerging remediation technology for such sites is the in situ immobilisation of radionuclides via biostimulation of dissimilatory metal reducing bacteria. While this approach has been successfully demonstrated in experimental studies, advances in understanding and optimization of the technique are needed. Mass transfer processes in heterogeneous and structured porous media may significantly affect the geochemical and microbial processes taking place in contaminated sites, impacting remediation efficiency significantly. The objective of this work was to understand better how heterogeneous porous media may affect immobilisation efficiency through interactions with the dominant geochemical, microbial and transport processes. A biogeochemical reactive transport model was developed for uranium immobilisation by DMRB. Physical heterogeneity is conceptually represented by a two-region model. Simulations investigate the parameter sensitivities of the system over wide ranging geochemical, microbial and groundwater transport conditions. The simulations highlight the conditions under which optimal remediation occurs. The relative significance of regional microbial residence patterns, U(VI)-surface complexation, geochemical conditions such as mineralogy, and porous media characteristics such as porosity and regional mass transfer are identified. Additionally, low level radioactive waste disposal sites typically contain significant quantities of cellulose, whose hydrolysis can have a significant impact on the geochemical conditions in these sites. Those geochemical conditions, in turn, can affect radionuclide mobility and bioimmobilisation. To investigate the potentially critical role of cellulose, process-based predictive model was developed, which includes a novel approach to biomass transfer between a cellulose-bound biofilm and biomass in the bulk liquid. A sensitivity analysis of the system parameters revealed the significance of bacterial colonisation of cellulose particles by attachment through contact in solution. The thesis concludes that the processes involved in uranium bioimmobilisation are sensitive to regional residence characteristics, media porosity, surface complexation, microbial efficiency, and mass transfer under varying conditions. Careful characterisation of potential sites and use of a model that includes these processes in sufficient detail is therefore deemed necessary before the remediation effectiveness can be reliably predicted.