The paper discusses the current prognoses of aquaculture development worldwide putting an emphasis on its effect on the environment and the issue of the protection of water reservoirs in different countries. Water consumption in diversified aquaculture systems is presented herein as well as the characteristics of the mechanical and biological water treatment methods in fish farms, with particular attention paid to the recirculating water systems. New aquaculture technologies using post-production waters are presented. The paper provides a discussion on the contribution of aquaculture to the global greenhouse gas emissions and the means of limiting this emission. The effect of climate change on aquatic ecosystems is presented in the context of the changes of the aquaculture production profile. The paper includes a brief presentation of the methods of mitigating the changes with respect to contamination of aquatic ecosystems as well as climate change. Reducing the water footprint can be achieved through selective breeding, species diversification and implementation of more technologically advanced aquaculture systems such as: integrated multi-trophic aquaculture, aquaponics and recirculation systems in aquaculture. The need for certification of fish farms with water recirculation systems is justified in the paper. The issues addressed herein are summarised and the main areas for extending the research promoting preservation of aquatic ecosystems in aquaculture are presented.