Radiolarian productivity pulses and related radiolarite deposition are phenomena difficult to understand from an exclusively actualistic viewpoint. Evolutionary selection pressure among silica-secreting marine plankton, both radiolarians and diatoms, has led toward more economic usage of rapidly shrinking nutrient resources, including dissolved silica, of the photic zone in the late Cenozoic oceans, and, in particular, a substantial modification of oceanic cycle by the diatom explosive radiation. Even if there is a proved link between biomineralization and dissolved silica loading among the phytoplankton only, the relative independence of modern siliceous planktic biotas from the available silica pool reflects mainly their progressive physiological specialisation during evolutionary history. Oceanic chemistry and productivity, as well as patterns of circulation/upwelling have changed radically during the Phanerozoic. Radiolarites apparently represent an 'anachronistic' facies, as exemplified by their long-lived and ocean-wide distribution in palaeo-Pacific, and hitherto, highlighted actualistic models of localized intra-oceanic wind-driven upwelling loci are of largely questionable applicability. In addition to plate drift, hypersiliceous domains and intervals are explainable mostly by a large-scale volcano-hydrothermal activity during major plate-boundary reconfigurations, which, in many ways, favoured siliceous biotas acme, and their skeletal remains accumulation and preservation. Factors tied to rapid, voluminous submarine eruptions, such as thermal buoyant megaplumes and basin overturns, offer a viable alternative for traditional climatic/circulation scenarios in case of hypersiliceous high productivity events irrelevant to greenhouse-to-icehouse climatic change. The evolving carbon and silica cycles were coupled through the greenhouse effect and enhanced chemical weathering. Volcano-hydrothermal and tectonic uplift events, related mostly to extensive rifting and/or accelerated oceanic spreading, were the endogenous driving force that created this perturbation of the exogenous system. The present biogeochemical cycle is representative only for the overall silica-depleted post-Eocene oceanic ecosystems, which broadly correlates with a major expansion of diatoms groups extremely efficient in silica removal, and closely linking the silica budget with phosphorus and nitrogen cycles. Thus, an orthodox uniformitarian approach to biosiliceous sedimentation, based on a silica-starved vigorous ocean, is of limited significance when applied to the pre-Neogene settings, especially in the peculiar planktic habitats of epeiric seas, as well as during biotic crises marked by strong geotectonic overprint. The major turnovers in marine siliceous biota composition, in particular after the end-Permian radiolarite gap, may have been coupled with discernible changes in an increasing biological control on the long-term oceanic silica cycling ('punctuated equilibrium'). The evolutionary turnovers have induced a stepdown decrease of dissolved silica levels through the Phanerozoic, contemporaneously with the general secular trend of upward scaling of nutrient-related ecological processes and increased effectiveness of resource utilization.