Water-in-salt (WiS) electrolytes are promising systems for a variety of energy storage devices. Indeed, they represent a great alternative to conventional organic electrolytes thanks to their environmental friendliness, non-flammability, and good electrochemical stability. Understanding the behaviour of such systems and their local organisation is a key direction for their rational design and successful implementation at the industrial scale. In the present paper, we focus our investigation on the 21 m bis(trifluoromethanesulfonyl)imide (LiTFSI) WiS electrolyte, recently reported to have acidic pH values. We explore the speciation of an excess proton in this system and its dependence on the initial local environment using ab initio molecular dynamics simulations. In particular, we observe the formation of HTFSI acid in the WiS system, known to act as a superacid in water. This acid is stabilised in the WiS solution for several picoseconds thanks to the formation of a complex with water molecules and a neighboring TFSI⁻ anion. We further investigate how the excess proton affects the microstructure of WiS, in particular, the recently observed oligomerisation of lithium cations, and we report possible notable perturbations of the lithium nanochain organisation. These two phenomena are particularly important when considering WiS as electrolytes in batteries and supercapacitors, and our results contribute to the comprehension of these systems at the molecular level.