Physical dormancy (PY), resulting from a water-impermeable seed coat, regulates germination timing in many angiosperms, including Dodonaea viscosa L. (Sapindaceae), a woody shrub widely distributed in tropical to warm temperate regions and coastal and inland habitats. Although PY has been previously documented in D. viscosa, the precise anatomical structure acting as the site for water entry, i.e., water gap, during dormancy release remains unclear. This study investigated the water gap’s morphology and function using microscopy, scanning electron microscopy (SEM) and imbibition assays. It also evaluate the effects of liquid nitrogen (LN₂) freeze–thaw cycles on seed coat integrity, dormancy break, and viability. Seeds possess a distinct hilar slit, which opens in response to hot-water treatment and serves as the exclusive water gap. Imbibition experiments showed that treated seeds (hot water , 10s) increased nearly 100% in mass over seven days, while control seeds absorbed no water. Further, covering the hilar slit with Vaseline restricted water uptake, confirming the absence of water-gap complex. Because the water gap opening was a small circular structure without any lid-like covering, it is classified as Type II. Seeds subjected to one or more liquid nitrogen (LN₂) freeze–thaw cycles experienced extensive seed coat cracking and severe damage to the embryo and cotyledons, leading to reduced viability and little to no germination. These findings demonstrate that while hot-water treatment effectively breaks dormancy, LN₂ exposure causes extensive mechanical injury and is ineffective for dormancy alleviation in D. viscosa. Thus, cryopreservation of some PY should be considered with caution.