In the current water treatment scenario, membrane filtration is a crucial technology due to its ability to effectively remove pollutants, ensuring clean and safe water. However, a significant challenge to its widespread application is membrane fouling, which reduces membrane efficiency and service life. Various membrane modifications have been studied to enhance fouling resistance. In this work, the effect of adding graphene oxide (GO) and molybdenum disulfide (MoS2) nanoparticles for the fabrication of mixed polyethersulfone (PES) membranes was evaluated. The modified membranes were evaluated for pollutant removal efficiency and fouling resistance using model humic acid solutions and surface water samples. The PES-GO membranes demonstrated significantly improved hydrophilicity, up to 43% reduction in protein deposition, and an average flux recovery ratio (FRR) of 63%, superior to the control PES membrane, resulting in reduced fouling and sustained high permeability. Nevertheless, although PES-MoS2 exhibited high rejection rates of dissolved organic matter and UV254, they also showed higher foulant adsorption and lower FRR, likely due to the development of a colloidal fouling when treating more complex water matrices. Attenuated Total Reflectance Fourier-Transform Infrared (ATR-FTIR) analysis confirmed the deposition of organic foulants, with polysaccharides and proteins identified as major contributors to fouling. These findings suggest that while GO-enhanced PES membranes offer improved water treatment performance, modifications with MoS2 require careful consideration of feedwater composition. Future work should focus on optimizing nanoparticle integration and evaluating membrane effectiveness for diverse water sources.