The accelerated growth of aquaculture has led to increasing demands for natural resources and ecosystem services, requires additional sites for expansion, and generates frequently observed environmental impacts. Accordingly, public concerns and socio-environmental conflicts have pushed key-role players to gradually adopt environmentally friendly practices. The aim of the present survey was to record and critically review (a) the environmental management practices applied in freshwater (land-based) and marine cage farms and (b) the awareness and perceptions of aquaculture producers related to fish-meal/fish-oil (FM/FO) replacement, organic farming, and poly-culture, including integrated multi-trophic aquaculture (IMTA) systems in Greece, which is the leading producing country of sea bass and sea bream in the Mediterranean. Environmental protection measures were applied by 82% of marine and by 60% of the freshwater farmers who responded. Moreover, principal components analysis (PCA) revealed that the overall environmental concern was positively correlated to the production capacity. Producers were generally familiar with FM/FO replacement and organic farming principles, although freshwater farmers were strongly opposed to the former practice based on fears for diminishing product quality. On contrary, poly-culture/IMTA concepts and benefits from their use were ignored by the majority of the producers. Finally, the survey demonstrated the important role of on-farm fishery/aquaculture scientists on these issues. To our knowledge, this is the first scanning of the perceptions of fish farmers on environmentally friendly practices, illustrating the variability in comprehension levels of such critical issues for the aquaculture industry.