This paper presents a large-scale modeling study characterizing fluid flow and tracer transport in the unsaturated zone of Yucca Mountain, Nevada, a potential repository site for storing high-level radioactive waste. The study has been conducted using a three-dimensional numerical model, which incorporates a wide variety of field data and takes into account the coupled processes of flow and transport in the highly heterogeneous, unsaturated fractured porous rock. The modeling approach is based on a dual-continuum formulation of coupled multiphase fluid and tracer transport through fractured porous rock. Various scenarios of current and future climate conditions and their effects on the unsaturated zone are evaluated to aid in the assessment of the proposed repository's system performance using different conceptual models. These models are calibrated against field-measured data. Model-predicted flow and transport processes under current and future climates are discussed.