The characteristics of acid migration through epoxy mortars were examined. Diffusion coefficients of typical sewer bio-metabolised acids: sulphuric, nitric, citric and oxalic acids were determined by gravimetric sorption method and fitted to the multi-phase Jacob–Jones model. Acid permeation was characterised by hindered pore diffusion with the extent being determined by the polarity of the acid and epoxy, and by the microstructure of the epoxy. Epoxy with higher polarity was able to reduce the diffusion coefficients by 49, while dense phases of the coating reduced the diffusion coefficient by 5,100. These results reflect the relative influence of epoxy polarity and microstructure on their performance as protective liners in sewers.