Application of updated diatom biochronology to the Monterey Formation and related biosiliceous rocks reveals the imprint of both global paleoclimatic/paleoceanographic and regional tectonic events. A rise in global sea level combined with regional tectonic deepening associated with the development of the transform California margin resulted in the abrupt onset of deposition of fine-grained Monterey sediments that were relatively free from clastic debris between 18 and 16 Ma. The base of the Monterey Formation does not mark a silica shift in diatom deposition from the North Atlantic to the North Pacific Ocean. Rather, a North Atlantic Ocean decline of diatoms after ca. 13 Ma and increasing divergence in nutrient levels between the North Atlantic and North Pacific Oceans between ca. 13 and 11 Ma coincided with a major enhancement of diatom deposition in the Monterey Formation. A stratigraphically condensed interval of phosphate-rich sediments between 13 and 10 Ma in coastal southern California appears to have resulted from sediment starvation in offshore basins during a period of higher sea level, as inland sections such as those in the San Joaquin Valley commonly contain thick sequences of diatomaceous sediment. Increasing latitudinal thermal gradients in the latest Miocene, which triggered a biogenic bloom in the equatorial Pacific Ocean at 8 Ma, also led to enhanced diatom deposition in the uppermost Monterey Formation and overlying biosiliceous rocks. Uplift of the California coastal ranges after ca. 5.2 Ma resulted in an increasing detrital contribution that obscured the presence of diatoms in onshore sediments. Major reduction in coastal upwelling in the early Pliocene ca. 4.6 Ma then caused a drastic reduction of diatoms in sediments offshore southern California.