Marine biofouling, the accumulation of organisms on underwater structures, presents challenges for aquaculture by increasing maintenance costs, impacting water quality, and affecting commercial species’ health. This study assessed biofouling levels on six net types star knotless normal knot nets (SN1, SN2), large black nylon knotless normal knot nets (NN), nylon knotless super knot nets (NS), Sapphire ultracore braided square nets (SU), and Sapphire SealPro braided square nets (SS) while investigating the influence of environmental factors on fouling development. Panels (1 m2) of each net type were deployed in an aquaculture farm for 23 weeks, during which biofouling mass, species composition, water temperature, pH, phosphate, and nitrate levels were monitored. A total of 70 species from 11 phyla were identified, with hydrozoans Aglaophenia tubiformis, Aglaophenia trifida, and Macrorhynchia philippina dominating the fouling community. Biofouling mass varied significantly among net types: dry weight ranged from 0.53 to 0.81 kg/m2, with organism densities between 9.63 and 12.22 individuals/cm2. SN2 exhibited the highest biofouling accumulation, significantly exceeding SU (by 0.267 kg/m2) and SS (by 0.297 kg/m2), while NN and SN1 exceeded SS by 0.20 kg/m2 and 0.173 kg/m2, respectively. Environmental analysis revealed that nitrate levels were negatively correlated with biofouling on SN2, NN, and SS, while temperature, pH, and phosphate had no significant effects. Notably, SS exhibited superior resistance to heavy fouling, with lower hydrozoan and tunicate settlement compared to other nets. The results underscore the importance of net material selection in aquaculture, as Sapphire nets demonstrated lower fouling rates, potentially reducing maintenance costs and environmental impact. Understanding biofouling dynamics and biodiversity interactions is essential for sustainable aquaculture practices and fostering a resilient blue economy.