This paper presents a review of a systematic research program for understanding scale and stress effects on transport behaviours of fractured crystalline rocks, using a hybrid discrete element and particle tracking approach. The motivation is the importance of understanding stress effects on behaviours of contaminant transport in fractured crystalline rocks, an important issue of rock mechanics for environmental safety assessments of many rock engineering projects. The study is divided into three steps. The first step is a basic study that established the mathematical platform for deriving the conditions, criteria, basic approaches and test case results for investigating stress and scale effects on hydraulic behavior of the fractured rock concerned. At the second step, based on outstanding issues drawn from the first step, the study was extended to consider effects of the correlation between the fracture aperture and size (represented by trace length) on the permeability of the fractured rock, and uncertainties in deriving equivalent continuum properties of fractured rocks. The third step added the particle/solute transport processes to the mathematical platform, including different retardation mechanisms, so that impact of stress on safety can be directly evaluated, even it can only be done conceptually. The obtained results show that stress, scale and inter-parameter correlations of the fracture system geometry are dominant issues for understanding and characterization of coupled hydro-mechanical processes of fractured rocks and play a significant role for understanding the mass transport behaviour in them, with direct impact on geo-environmental safety.