The properties of water molecules in nanoconfined geometries have significant roles in different fields such as adsorption, electrochemistry, biology, earth science, materials science, and nanofluidic devices. In this work, water molecules confined between parallel graphene plates and also confined into carbon nanotubes (CNTs) doped with (3 and 20%) B, N, and Si atoms have been studied using molecular dynamics (MD) simulations. Some structural, thermodynamics, and dynamical properties of the water molecules were studied in the different systems with different densities. At low densities, the 20% Si-doped system has the least number of hydrogen bonds (HBs) whereas it has the most number of HBs at higher densities. The high N- and Si-doped CNTs have also more HBs than the other CNT systems. Also, the water molecules into the high N-doped CNT represented more ordered pentagonal shapes than the other CNT systems. The structural examinations using the O–H and O–O radial distribution functions (RDFs) of both graphene and CNT systems approved the HB results. The self-diffusions of confined molecules in high Si-doped graphene and CNT systems were smaller than the other doped systems. A density-dependent and a temperature-dependent phase transition have been also observed in the doped graphene and CNT systems, respectively. The effects of doped atom distribution, pore size, and temperature have been also investigated.