Sodium hydroxide (NaOH) has been shown to result in fast nucleation of highly monodispersed silica nanoparticles (SNPs). However, limited work has been reported on the physicochemical properties of the resulting SNPs and their surface modification. Herein, we demonstrate that NaOH results in poor hydrolysis of silica precursor, SNPs with adsorbed sodium ions and thermally unstable siloxane cross-linkage. The sodium ions are removed by refluxing SNPs in a 4 vol% hydrochloric acid solution. This step was also found to significantly improve the thermal stability of SNPs. The surface chemistry of the SNPs was easily modified with 0.74 mmol/g of octyltrimethoxysilane and 0.42 mmol/g of octadecyltrimethoxysilane. Functionalised SNPs exhibited superhydrophobicity (water contact angle ≥150°) and displayed a decrease between 2.46% to 3.03% in moisture sorption at 95% relative humidity. The results reveal that the acid treatment will be crucial in the design of hydroxylated and thermally stable SNPs from NaOH-catalysed synthesis.