The fishing fleet of European Union (EU) nations gets billions in tax benefits each year, and the combustion of that fuel results in millions of tons of carbon emissions each year—and quantity of carbon dioxide equal to what Malta's entire fishing fleet emits each year. By considering the function of fishing output, fossil fuel usage, economic development, and population density (PD) from 1990 to 2022, this study examines the dynamic impact of the fishery sector on blue carbon in 27 European nations. The findings revealed a significant positive correlation and showed a significant positive association between fishing output as well as carbon sink decline at most quantiles by adopting an innovative methodology which is the method of moments quantile regression method which has a fixed factor. From the first to the ninth quantiles, fishery output greatly accelerates the decline of blue carbon storage, with a more substantial impact at the highest and a lesser influence at the lowest quantile. The findings also show that the EU14 developed countries experience a more meaningful, beneficial effect of fishing output on carbon sink deterioration than the EU13 developing nations. Economic development in EU14 created and EU13 developing nations were found to compress carbon sink degradation across all quantiles, supporting the growth theory for countries that produce fisheries. Fossil fuel usage was found to boost carbon sink degradation. In EU14 developed countries, the impact of PD was significantly negative from the first to the seventh quantiles. In contrast, in EU13 developing countries, this has a significant positive effect across all quantiles. With the help of diverse and green energy sources like the tide and wave energy, lawmakers can reduce the deterioration of blue carbon in the EU14 and EU13 nations.