Two water-stable zirconium-based metal-organic frameworks (MOFs) (NU-1000 and UiO-67) have been synthesized in various size scales (100-2000 nm) for the adsorptive removal of glyphosate from the aqueous media. Both NU-1000 and UiO-67 possess a three-dimensional structure; NU-1000 consists of triangular micropores and wide mesoporous channels (31 Å), whereas UiO-67 has cage-like pores [octahedral (16 Å) and tetrahedral (14 Å) cages]. NU-1000 comprises Zr6(μ3-O)4(μ3-OH)4(H2O)4(OH)4, and UiO-67 contains Zr6O4(OH)4 as secondary building units. These units act as Lewis acid nodes and can interact with the Lewis base phosphate group of the glyphosate. The time taken for reaching equilibrium is found to be reduced considerably as the size of the MOF decreases. The smaller the particle size, the lesser is the diffusion barrier for the analyte, which enhances the interaction between Lewis acidic metal nodes and the Lewis basic center of the glyphosate molecule. NU-1000 was found to be better compared to UiO-67, both in terms of efficiency and reusability. This might be due to the larger pore diameters of the NU-1000. Theoretical calculations revealed that the interaction energy of glyphosate with the nodes of NU-1000 is higher (-37.63 KJ mol-1) compared to UiO-67 (-17.37 KJ mol-1), which might be the possible reason for the higher efficiency of NU-1000.