In the current study, pristine PVDF nanofibre membranes were successfully modified with silica nanoparticles (SiO2NPs) or with organically-functionalised (silanised) silica nanoparticles (f-SiO2NPs). The superhydrophobic f-SiO2NPs-modified PVDF membranes (contact angle = 156 ± 6°) showed enhanced water flux and lower flux decays than those of pristine and SiO2NPs-modified PVDF membranes under both low salinity (LS) and high salinity (HS) feed solution conditions. Nevertheless, the higher organic content of the LS feed exacerbated fouling and wetting in both pristine and modified membranes (i.e., flux decays of up to 73.6% in uncoated membrane samples). These results indicate the efficiency of the silanisation of f-SiO2NPs in attaining super-hydrophobicity and enhanced performance in modified PVDF membranes. However, fouling and wetting still had a negative impact on the performance of the f-SiO2NPs-modified PVDF membranes. To provide anti-fouling properties, a hydrophilic layer consisting of silver nanoparticles (AgNPs) and functionalised multi-walled carbon nanotubes (f-MWCNTs) was coated on the pristine and modified membranes. This layer significantly decreased the flux decay and enhanced the resistance towards a decay in salt rejection of pristine, SiO2NPs-modified, and f-SiO2NPs-modified PVDF membranes under both LS and HS feed solution conditions. The adsorption of foulants also changed the surface characteristics of both coated and uncoated membranes, as evidenced by a decrease in contact angle and increase in interfacial free energy. The hydrophilic coating layer provided fouling-resistance properties, high salt rejection, and low flux decays to hydrophobic PVDF nanofibre membranes, demonstrating the high potential of this technique to produce potable water from brackish water in Membrane Distillation processes.