A series of flexible metal-organic frameworks (MOFs) belonging to the MIL-53 family, such as MIL-53(Al), its amino-functionalized analog NH2-MIL-53(Al), and MIL-53(Al) type materials with Al3+ ions and mixed benzene-1,4-dicarboxylate and 2-aminobenzene-1,4-dicarboxylate linkers (MixLR) in various proportions were prepared in a nanocrystalline form using MW-activation under atmospheric pressure according to the original solvothermal procedure. The MIL-53(Al) and NH2-MIL-53(Al) samples feature nanocrystals with sizes of 200-300 nm, while MixLR matrices synthesized in this manner are composed of small nanoparticles with sizes of about 20-30 nm. MIL-53(Al) type materials (MIL-53(Al), NH2-MIL-53(Al) and MixLR) were probed in the adsorption of a typical herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in an aqueous medium. This study revealed a strong impact of the flexibility and porosity of the synthesized MIL-53(Al) type matrices on their physicochemical characteristics. MIL-53(Al) type materials show much higher 2,4-D adsorption rates than an activated carbon matrix (CSAC). The structural characteristics of the studied MIL-53(Al) type materials were established with a high resolution X-ray powder diffractometer equipped with a synchrotron radiation source. The obtained results can be used for the development of advanced adsorbents based on MIL-53(Al) type materials for water remediation.