The detailed study of diatom laminations conducted by means of backscattered electron imaging serves as tool to unravel details of past ocean dynamics. In this paper we apply this method to the analysis of the diatomites of Cerro Los Quesos, Upper Miocene Pisco Fm, Peru. Numerous studies have been conducted on the Pisco Fm; however, a focus on its paleoceanographic significance is still lacking. In this work, we provide information on the oceanographic setting in the area at the time of diatomites deposition. The high abundance of deep‐living Coscinodiscus laminae, proceeded by either a mixed lamina or a terrigenous one, let us hypothesize a deep position of the thermocline during the deposition of the Pisco diatomites; together with the scarcity of Chaetoceros Hyalochaete spp. resting spores, this evidence confutes the belief that equals high biogenic silica content in marine sediments with enhanced upwelling. Conversely, the depositional setting of the Pisco Fm diatomites is more similar to what is known as “permanent El Niño” (or “El Padre”) state, meaning a constant weakened upwelling (or upwelling of nutrients‐poor waters). Climate modeling warns that an increase in atmospheric CO2 may lead to this mean state in the near future. Thanks to this study we also obtained refined information on the diatomites sedimentations rates. The comparison of the Pisco diatomites sedimentation rates with those of Quaternary diatomites gave strength to the hypothesis that the formation of the vertebrate Lagerstätte may have been enhanced, among others, by the so‐called “impact‐burial” mechanism.