The assessment of the effects of aquaculture and fisheries on greenhouse gas (GHG) emissions is crucial, especially within the framework of environmental sustainability and global efforts to mitigate climate change. This study investigates the effect of the aquaculture industry, Blue R&D, green energy, and maritime transport on GHG emissions in Ireland and Norway from 2000 to 2019 using quantile-on-quantile regression (QQR) and wavelet coherence (WC). The results of the QQR model indicate a negative effect of aquaculture production at a lower quantile in Ireland. However, the effect turns positive at upper quantiles, showing that aquaculture increases GHG emissions. The strict regulation and efforts to address sustainable aquaculture practices can explain the impact of aquaculture production on GHG emissions in Norway. Maritime transport positively affects GHG emissions in both countries, yet the blue R&D seems more considerable in Norway than in Ireland. The causal relationship between variables implies a substantial impact of the explanatory factors on GHG emissions that have policy directions for policymakers and investment managers.