Surficial silicifications have been long considered to be indicative of warm and dry climates. Here we describe various forms of supergene silicification in a Miocene lacustrine sequence in the Missour Basin near Jbel Ghassoul (Morocco) in a landscape with accentuated relief. The silicification is almost exclusively limited to a 10–40 m wide zone from the edges of scarp and mesa landforms. This distribution is interpreted to record the locations where groundwaters which produced the silicification discharged from a higher level palaeolandscape. The main component of the silica was imported late and significantly post-dates the deposition of the sediments. This implies that significant volumes of silica-bearing solutions flowed through these formations in response to a hydraulic gradient generated by relief. Silicification thus occurred only after uplift and incision of the sedimentary fill of the Missour Basin. The zones of silicification of the Jbel Ghassoul sequence can be linked geomorphologically to remnants of high-level pediments that have been dated in the literature to the early to middle Pleistocene and interpreted to have been formed during cold climates. Low temperatures in outcrops near the discharge zones during cold periods are considered to be a key factor in silica precipitation from groundwaters.