Application of mesoporous silica nanoparticles (MSNs) as antifouling/antibacterial carriers is limited and specifically with a dual synergetic effect. In the present work, MSNs modified with quaternary ammonium salts (QASs) and loaded with the biocide Parmetol S15 were synthesized as functional fillers for antifouling/antibacterial coatings. From the family of the MSNs, MCM-48 was selected as a carrier because of its cubic pore structure, high surface area, and high specific pore volume. The QASs used for the surface modification of MCM-48 were dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride and dimethyltetradecyl[3-(triethoxysilyl)propyl]ammonium chloride. The QAS-modified MCM-48 reveals strong covalent bonds between the QAS and the surface of the nanoparticles. The surface functionalization was confirmed by Fourier transform infrared spectroscopy, thermogravimetric analysis, elemental analysis, and ζ-potential measurements. Additional loading of the QAS-modified MCM-48 with a commercially available biocide (Parmetol S15) resulted in a synergetic dual antibacterial/antifouling effect. Either loaded or unloaded QAS-modified MSNs exhibited high antibacterial performance confirming their dual activity. The QAS-modified MCM-48 loaded with the biocide Parmetol S15 killed all exposed bacteria after 3 h of incubation and presented 100% reduction at the antibacterial tests against Gram-negative and Gram-positive bacteria. Furthermore, the QAS-modified MCM-48 without Parmetol S15 presented 77-89% reduction against the exposed Gram-negative bacteria and 78-94% reduction against the exposed Gram-positive bacteria. In addition, the modified MCM-48 was mixed with coating formulations, and its antifouling performance was assessed in a field test trial in northern Red Sea. All synthesized paints presented significant antifouling properties after 5 months of exposure in real seawater conditions, and the dual antifouling effect of the nanoparticles was confirmed.