Middle and Upper Eocene biogenic sediments in the Willunga Embayment along the eastern margin of the St Vincent Basin are a series of warm-temperate limestones, marls and spiculites. The Middle Eocene Tortachilla Limestone is a thin, coarse grained, quartzose, biofragmental, bryozoan–mollusc calcarenite of stacked metre-scale depositional cycles with hardground caps. Lithification, aragonite dissolution and the filling of moulds by sediment and cement characterize early marine-meteoric diagenesis. Further meteoric diagenesis at the end of Tortachilla deposition resulted in dissolution, Fe-oxide precipitation and calcite cementation. The Upper Eocene Blanche Point Formation is composed of coccolith and spiculite marl and spiculite, all locally rich in glauconite, turritellid gastropods and sponges. Decimetre-scale units, locally capped by firmgrounds, have fossiliferous lower parts and relatively barren upper parts. Carbonate diagenesis is minor, with much aragonite still present, but early silicification is extensive, except in the spiculite, which is still opal-A. All depositional environments are interpreted as relatively shallow water: high energy during the Middle Eocene and low energy during the Upper Eocene, reflecting the variable importance of a basin-entrance archipelago of carbonate highs. Marls and spiculites are interpreted to have formed under an overall estuarine circulation system in a humid climate. Basinal waters, although well mixed, were turbid and rich in land-derived nutrients, yet subphotic near the sea floor. These low-energy, inner-shelf biosiliceous sediments occur in coeval environments across other parts of Australia and elsewhere in the rock record, suggesting that they are a recurring element of the cool-water, carbonate shelf depositional system. Thus, spiculites and spiculitic carbonates in the rock record need be neither deep basinal nor polar in origin. The paradox of a shallow-water carbonate–spiculite association may be more common in geological history than generally realized and may reflect a characteristic mid-latitude, humid climate, temperate water, palaeoenvironmental association.