Anthropogenic emissions of mercury to the environment are of great concern due to its toxicity. The burning of coal contributes highly to Hg emissions and, as such, much lower effluent discharge limits for Hg in flue gas desulphurisation (FGD) wastewater have recently been proposed in the USA. Lower detection limits are required to meet the most demanding discharge limit of 10 ng L−1. Therefore, in this work, a new analyser for online monitoring of Hg in FGD wastewater based on syringe injections of chemicals combined with gold amalgamation – atomic fluorescence spectrometry has been developed. The instrument has been validated against international standard method ISO 17852, as well as an interference study with extreme levels of salts majorly present in FGD water. Detection limits of 1.8 ng L−1 as well as accurate performance in an on-site field trial indicate that the methodology is fit to meet the new legislation.