Metal-catalysis in aqueous medium has led in recent years to the development of a huge number of new and greener synthetic methodologies in organic chemistry. Also, the search for organic reactions that proceed with efficiency, selectivity and atom economy has emerged as a prime goal in synthetic chemistry. Among the organic processes that take place with atom economy, isomerization reactions are typical examples because no by-products are generated. In this regard, the isomerizations of readily accessible allylic and propargylic alcohols, mainly giving carbonyl compounds, provide a simple synthetic route to these very valuable raw materials in organic chemistry. In this review, an overview of the progress achieved on the catalytic isomerization of allylic and propargylic alcohols in environment-friendly aqueous media will be presented.