Three-dimensional seismic data from the NE Atlantic margin have revealed opal-A to opal-CT reaction zones hosted in Oligo-Pliocene strata as bright reflection events that cross-cut stratigraphic reflections. In some areas, the topographic relief at the top of the reaction zone has a remarkable geometry comprising roughly circular flattish regions, spaced 1–3 km apart, separated by networks of steep-sided troughs or ridges with a relief of up to 200 m. Here we show that these topographic structures formed around the upper tips of polygonal faults, and that remnants exist at deeper stratigraphic levels below the opal-A to opal-CT cross-cutting reflection. Furthermore, we deduce that the chemistry of formation water expelled transiently through the polygonal faults must have played a key role in their formation. Within silica-bearing successions, the transformation of opal-A to opal-CT is followed by the transformation of opal-CT to quartz at greater depth. The opal-CT to quartz transformation releases magnesium, which is known to promote opal-A to opal-CT transformation at lower temperatures. Consequently, we suggest that when the opal-A to opal-CT reaction zone nears the top of the polygonal fault system, it advances more rapidly through strata flushed by pore water that is richer in magnesium.