The extensive presence of microbial cells in aquatic sediments and the complex interactions/aggregations with sediment particles are found to have substantial effects on the dynamic processes of sediment transport. To date, extensive efforts have been paid to investigate such complex but typically common processes, but we are still far from a clear understanding. Specifically, the three-dimensional (3D) matrices of biosediment association, microbial mediation in the enhancement and reduction of sediment stability, and the effects of bio-sediment association on drag and settling velocities, remain to be clearly understood. This thesis seeks for a clearer and more comprehensive understanding of microbial sediment interactions and the influences on the resuspension and deposition processes of sediment transport. To achieve these goals, a new approach has been developed by using X-ray microtomography techniques, which for the first time allows the 3D matrices of biological sediment aggregates (BSA) to be imaged and quantified in their hydrated states. The results show that the microbial development state and the complex microbial sediment interaction/aggregation can significantly affect BSA architectures. As the BSA grow towards a better developed state, with higher organic fractions and larger aggregated sizes, the internal structure of BSA appears to become more compact and interconnected. The BSA at different stages of development in turn have a range of effects on sediment stability. The more fully developed BSA of a high organic fraction are found to biostabilize sediments, while the BSA at a less well developed state with lower organic fractions considerably destabilize sediments. By contrast, the microbial influences on the depositional processes present different patterns, where the volume of pore water plays a more important role in determining settling velocities, compared to the organic matter. These important results reveal the mechanisms and properties that influence microbial moderations of resuspension and deposition processes, providing much needed insight into microbial sediment transport. Predictive relationships for estimating the stability, drag and settling velocities of BSA are also tentatively proposed based on the test data available. The insights gained suggest important possibilities for future work to achieve a more complete characterization of sediment transport in the presence of microbial mediation.