In the sections at Shell Beach (Pismo Basin) and Mussel Rock (Santa Maria Basin)—both along the central California coast—the Miocene Monterey Formation is composed of laminated, biosiliceous, organic-rich and phosphate-rich sediments, which are intercalated with carbonates and volcanogenic deposits. The presence of small- and large-scale scours, conglomerates, gravity-flow deposits, slumps, and condensed intervals reveals the importance of sediment reworking, which is related to the presence of bottom currents, the general morphology of the basins, and recurrent high-energy events of likely seismic origin. The lithologies reflect strong upwelling, enhanced primary productivity, and the presence of an oxygen-minimum zone, which is indicated by ubiquitous lamination, a general absence of bioturbation (with the rare exception of traces related to the gravity-flow displacement of trace makers), high pyrite, Mo, and U concentrations, and molar ratios of total organic carbon and organic phosphorus (TOC/Porg) of up to 2000. Oxygen depletion was particularly severe during the early Langhian, and the late Serravallian and early Tortonian, and favored the preservation of organic matter. Episodes of deposition of organic-rich sediment were followed by longer phases of subdued sediment accumulation and early diagenetic phosphogenesis, which resulted in the formation of a low-porosity, less permeable “lid” in the near-surface sediments that assisted in preserving organic matter. Phosphogenesis occurred throughout the time interval considered (approximately 17.5–6.5 Ma), and phosphate-rich sediments formed especially during periods of sedimentary condensation in the Langhian and earliest Serravallian, and the latest Tortonian and early Messinian. A comparison of temporal trends in the type and quantity of deposited sediments between the two sections at Shell Beach and Mussel Rock, and three sections of the Santa Barbara Basin (El Capitan State Beach, Naples Beach, and Haskell Beach) confirms that towards the top of the Monterey Formation, sediments become enriched in biosilica in all three basins. The transition into this lithology occurred diachronously, during the Serravallian in the Pismo and Santa Maria basins and Tortonian in the Santa Barbara Basin, and was probably related to a diachronous shift to more intense upwelling in all three basins. A phase of important condensation and phosphogenesis terminated Monterey-“type” sedimentation during the latest Tortonian and early Messinian in both the Santa Maria and Santa Barbara basins. The uniform expression of this phase is interpreted as the result of improved connections between the two basins.