We provide experimental evidence for confinement of water molecules in the pores of hexagonal structure of YPO₄ at elevated temperatures up to 600 K using powder neutron diffraction. In order to avoid the large incoherent scattering from the hydrogen, deuterated samples of doped YPO₄:Ce-Eu were used for diffraction measurements. The presence of water molecules in the triangular and hexagonal pores in the hexagonal structure was established by detailed simulation of the diffraction pattern and Rietveld refinement of the experimental data. It was observed that the presence of water leads specifically to suppression of the intensity of a peak around Q = 1.04 Å⁻¹ while the intensity of peaks around Q = 1.83 Å⁻¹ is enhanced in the neutron-diffraction pattern. We estimate the number of water molecules as 2.36 (6) per formula units at 300 K and the sizes of the hexagonal and triangular pores as 7.2 (1) and 4.5 (1) Å, respectively. With an increase in temperature, the water content in both pores decreases above 450 K and vanishes around 600 K. Analysis of the powder-diffraction data reveals that the hexagonal structure with the pores persist up to 1273 K, and transforms to another structure at 1323 K. The high-temperature phase is not found to have the zircon- or monazite-type structure, but a monoclinic structure (space group P2/m) with lattice parameters a_m = 6.826 (4) Å, b_m = 6.645 (4) Å, c_m = 10.435 (9) Å, and β = 107.21(6)°. The monoclinic structure has about 14% smaller volume than the hexagonal structure which essentially reflects the collapse of the pores. The phase transition and the change in the volume are also confirmed by x-ray-diffraction measurements. The hexagonal-to-monoclinic phase transition is found to be irreversible on cooling to room temperature.