The pollution of water has become an emergency problem on the world scale. The pollutants come from different sources and have various characteristics, including industry and sewage. Diverse sources of pollution require a comprehensive approach to water purification. One of the most promising, taking into consideration the idea of sustainable development, is bioremediation systems. This article is focused on current research in the area of fungi application for bioremediation purposes, especially in the area of water treatment. The main aim of the article is to present the future scope of fungal bioremediation systems, taking into consideration the up-to-date challenges and perspectives for their development. This chapter is based on the systematic literature review and some case studies. It shows the last research in this area together with the estimation of practical estimation of these technologies. The advantages and disadvantages are presented. Additionally, some information about changing trends in water treatment technologies is shown. The chapter is complete, with a short discussion about the current tendencies on the market and possible future directions for fungal remediation technologies development.