We report on formation of gypsum scale from the concentrate of a desalination plant despite the presence of a phosphonate antiscalant (PermaTreat 191). Batch experiments were conducted in order to study the relevant chemical conditions that lowered the effectiveness of this antiscalant and led to the formation of the scale. It is shown that the antiscalant is effective in postponing nucleation and hindering crystal growth of gypsum in the supersaturated concentrate with a neutral pH. However, as pH decreases both nucleation and crystal growth accelerate. In this specific desalination plant, a sharp drop in concentrate pH occurs when an acidic effluent, a byproduct of a boron removal facility, is added in small amounts. The pH effect on gypsum crystal growth, even at circum-natural pH values, is gradual. This gradual trend suggests that protonation of the antiscalant functional groups lowers antiscalant adsorption to gypsum and hence represses its effectiveness.