Although clinicians use fluoride agents to reduce the occurrence of caries, and surface sealing agents to protect composite restorations, the effects of these agents on composite resins have not yet been investigated. The goal of this study was to determine the effect of different surface applications (fluoride or surface sealant) on resin composites with different organic structures (Siloranes, Sonicfill, 3M Z550, Kalore). In this study, 120 discs and 120 bars made of composite resin were stored in water for three months before being thermally aged by cycling between 5°C and 55°C for 10,000 cycles. The discs were 15 mm in diameter and 1 mm thick; the bars were 25 × 2 × 2 mm. The surface sealant and fluoride were applied to the specimens, and evaluations were performed after 24h. Initial and final calculations were performed for flexural strength, microhardness, roughness, gloss, water sorption, and solubility. Silorane composite showed the lowest water sorption levels (p < 0.05) for both initial and aged groups. Silorane and SonicFill composite groups showed the lowest solubility (p < 0.05). Both before and after aging, the SonicFill group showed the highest values of flexural strength and microhardness. Silorane showed the highest roughness and lowest gloss values. Lower water sorption and solubility rates were seen on materials fabricated from hydrophobic monomers. High water sorption and solubility degrades the mechanical and surface properties. Fluoridation and surface sealant application can alter the surface properties but do not have any effect on the mechanical properties.