Mechanisms of coupled hydro-bio-chemo-mechanical phenomena play an important role in many natural and engineered processes in granular soils. The present work studies two seemingly distinctly different processes which share a common thread in their need for addressing the effect of non-mechanical phenomena across scales. Firstly, desiccation shrinkage of drying soils is investigated via a hydro-geomechanical multi-scale model. This research aims to identify and quantitatively evaluate various critical mechanisms associated with the processes of desiccation shrinkage and cracking in drying silty soils. A previously developed 1D bundle-of-tubes model is refined to simulate the various stages of drying shrinkage in 2D, using the actual pore size distribution based on mercury intrusion porosimetry (MIP) data. It is revealed that the resulting shrinkage evolution is affected by air entry that may occur in two possible scenarios: air incursion at the external surface and formation of vapor nucleus in the interior. The analysis of mechanical deformation is coupled with the numerical simulation of the drying process which can be often characterized as a two-stage development, consisting of a constant rate period and a falling rate period. Numerical simulation of the drying rate evolution suggests that it may be closely associated with the onset of air entry and/or the progress of desaturation. Further transition of solid- water structural configuration into funicular and pendular states from initially capillary state is simulated. The second topic investigated is the coupled bio-chemo-geomechanical mechanisms through a discrete element modelling approach. Bio mediated soil improvement method based on microbial induced calcite precipitation (MICP), can be a sound technique for modifying soil properties such as strength, stiffness and permeability. This portion of work focuses on establishing the bio-chemo-mechanical coupling effects at the micro scale and explores the macro-scale response of sandy soil using distinct element method as a modeling tool. The bio-chemo-mechanical interaction process may strongly affect the mechanical response and transport properties of geomaterials. Such interaction is believed to occur at the granular scale but its effects are often manifested at higher scales. A rate law is introduced for the mass of calcite precipitated due to the bio treatment of soil, and is linked to a change in stiffness of bonded precipitated material, which is implemented in Particle Flow Code (PFC2D). A parallel bond feature available in PFC2D is used to model the effect of cementitious material. A reasonable amount of increase in strength due to calcite precipitation is achieved for the sandy soil used.