The density of soil water exhibits significant variation, yet no comprehensive theory currently exists to fully explain this pattern. In this study, quartz tubes with micrometer-scale diameters were used to simulate the pore systems of porous media, and the mass-volume method was employed to measure the density of water in eight quartz tubes with diameters ranging from 50 μm to 530 μm. The results indicate that when the diameter of the quartz tube is less than 75 μm, the density of water exceeds that of bulk water, reaching a maximum of 1.19 g/cm. Conversely, when the diameter ranges between 100 μm and 250 μm, the density of water is slightly lower than that of bulk water, with a minimum of 0.98 g/cm. The variation in water density with quartz tube diameter can be described using an empirical formula similar to the Lennard-Jones potential. The findings suggest that conventional mechanisms such as hydration effects, water-solid interfacial interactions, capillary effects, or cavitation cannot fully account for the observed changes in water density within the quartz tubes. Instead, the analysis indicates that the complex hydrodynamics and rheology within the capillaries: particularly shear thickening at the tube nozzle and its reverse process may be the primary physical mechanism driving the changes in water density across quartz tubes of different diameters. This mechanism represents a departure from traditional theories used to explain variations in soil water density and offers a novel perspective for understanding the phenomenon. It becomes possible to predict the density of water in soils with varying water contents by integrating the observed variation in water density within quartz tubes with soil water content models based on the concept of capillary bundles in porous media. Future research should focus on the fundamental principles of rheology to establish quantitative relationships between shear rate and viscosity, as well as between viscosity and density. Such efforts would enable the theoretical construction of models to describe the density variation of capillary water and soil water.