The cultivation of Gracilaria chilensis ("pelillo") is an important aquaculture industry in Chile, but the growth of epiphytic algae threatens its productivity. This study investigates the spatio-temporal dynamics of epiphytic algae in G. chilensis farms in the Pudeto and Maull & iacute;n rivers, Los Lagos Region, Chile, from 2017 to 2021. Seasonal sampling assessed epiphyte biomass, taxa richness, and their impact on the seaweed's growth. A total of 21 species of epiphytes were identified, with 14 found within the sampling quadrats and seven outside. Significant seasonal fluctuations in wet biomass and taxa richness were observed, with the highest epiphyte load recorded during the summer months, particularly in the Pudeto river. Here, the epiphyte load was consistently higher than Maull & iacute;n's, which showed no significant annual changes in 2017 but a notable increase in epiphyte biomass by 2021, even during winter. Canonical Correspondence Analysis (CCA) revealed that environmental factors, such as salinity, significantly influenced epiphytic assemblages. Lower salinity sites promoted Chaetomorpha linum, Grateloupia sp., and Ulva sp., while more marine conditions supported Polysiphonia sp. and Ulva sp. These findings highlight the need for targeted management strategies to mitigate epiphyte proliferation, ensuring the sustainability of G. chilensis farming. Effective intervention measures, including improved farming practices and environmental monitoring, are critical to reducing economic losses and maintaining the viability of this important aquaculture resource.