As global temperatures rise and become more variable, the capacity of farmed species to adapt while maintaining production efficiency is becoming a pressing concern. Aquaculture species are particularly vulnerable due to their exposure to heightened variation in natural aquatic environments. In this context, Genotype-by-Environment (GxE) interactions pose a significant logistical challenge for selective breeding, as traits that perform well in one environment may not in another. These interactions complicate the design of breeding programs that aim to ensure long-term resilience while optimizing short-term productivity. Genomic offsets, a novel metric that quantifies the genetic changes required for populations to adapt to anticipated environmental shifts, may offer a promising solution. Here, we explore potential applications of genomic offsets in aquaculture, including their use as tools for risk assessment, selective breeding, and cryopreservation. We will also discuss how genomic offsets can overcome the hurdles posed by GxE interactions, addressing practical considerations such as data requirements and methodological frameworks, and needed validation efforts. By predicting maladaptation risks and guiding the selection of individuals best suited for changing environmental conditions, genomic offsets may help breeders proactively enhance genetics for long-term resilience of aquaculture species.