A highly efficient nanofiltration membrane should exhibit high separation performance in removing divalent salts and organic solutes, as well as high permeation to meet practical separation and purification applications in aqueous media. Here, we designed a series of hybrid multilayer thin film membranes filled with the structurally and morphologically different nanofillers such as hexagonal boron nitride (HBN) nanosheets and metal-organic framework (MOF) nanoparticles, consisting of 3 and 6 layer pairs of polyelectrolyte through the layer-by-layer self-assembly technique (LBL) and characterized them in terms of dye and salt separation, as well as permeation. The rejection performance and permeability of the designed membranes manifested that HBN nanosheets were more effective than MOF nanoparticles in achieving a high-performance membrane. As compared to the bare multilayer thin film membrane, the addition of HBN nanosheets within the negatively-charged layers of the multilayer thin film membrane consisting of 6 bilayers resulted in good retention of up to 93% and 92% for acid blue (ACB) and bromophenol blue (BPB) dye molecules, respectively. Besides, this membrane exhibited 60% and 45% improvement in the water flux for ACB and BPB solutions, respectively, while the rejection of the sulfate ions maintained an acceptable value around 78%. Furthermore, it was found that this HBN-embedded hybrid multilayer membrane had superior potential for the removal of coherent foulant compared to all samples.