Mercury (Hg), and in particular its methylated form (methylmercury, MeHg), is a hazardous substance with the potential to produce significant adverse neurological and other health effects. Enhanced anthropogenic emissions and long-range transport of atmospheric Hg have increased Hg concentrations above background levels in aquatic systems. In this context, the Minamata Convention, a global legally binding agreement that seeks to prevent human exposure to Hg, was signed and enforced by 128 countries, and today more than 90 Parties have ratified it. All these Parties have committed to develop Hg monitoring programs to report the effectiveness of the convention. For this purpose, we provide a standardized cleaning and water sampling protocol for the determination of total-Hg and MeHg in freshwaters at ambient levels. As Hg and organic matter are tightly bound, the protocol also describes sample collection for dissolved organic carbon (DOC) concentration and characterization of dissolved organic matter (DOM) composition by fluorescence spectroscopy. This protocol is highly useful to non-experts without a prior background in Hg sampling and analysis, and can serve as a useful basis for national monitoring programs. Furthermore, this protocol should help increase quantitative inventories of DOC, inorganic-Hg (IHg) and MeHg concentrations and DOM composition in freshwater, which are severely lacking at a global scale.