The unsaturated zone at Yucca Mountain, a potential repository site of high-level nuclear waste, is a complex hydrologic system in which a variety of important flow and transport processes is involved. To quantify these processes as accurately as possible is a theoretically challenging and practically important issue. In this study, we propose a new formulation for modeling flow and transport in unsaturated fractured rocks. The formulation is mainly based on a hypothesis that only a portion of connected fractures are active in conducting water. Analysis of the relevant data with the new formulation suggests that about 18–27% of the connected fractures in the Topopah Spring welded (TSw) unit (the potential repository unit) of Yucca Mountain are active under ambient conditions. The relatively high percentage of active fractures is consistent with field observations from a variety of sources. Sensitivity analyses are performed to investigate effects of the “activity” of connected fractures on flow and transport behavior in unsaturated rocks.