Eutrophication has become one of the major environmental issues of global concern due to the adverse effects on water quality, public health and ecosystem sustainability. Fundamental research on the restoration of eutrophic freshwaters, i.e., lakes and rivers, is crucial to support further evidence-based practical implementations. This Special Issue successfully brings together recent research findings from scientists in this field and assembles contributions on lake and river restoration. The 12 published papers can be classified into, and contribute to, three major aspects of this topic. Firstly, a background investigation into the migration of nutrients, and the characteristics of submerged biota, will guide and assist the understanding of the mechanisms of future restoration. Secondly, various restoration strategies, including control of both external and internal nutrients loading, are studied and evaluated. Thirdly, an evaluation of the field sites after restoration treatment is reported in order to support the selection of appropriate restoration approaches. This paper focuses on the current environmental issues related to lake and river restoration and has conducted a comprehensive bibliometric analysis in order to emphasise the fast-growing attention being paid to the research topic. The research questions and main conclusions from all papers are summarised to focus the attention toward how the presented studies aid gains in scientific knowledge, engineering experience and support for policymakers.