A protocol is described for separating sub-20 microm-sized particles contained in sedimentary rocks into size fractions. Geochemical data from manually isolated foraminifera are commonly used in the interpretation of marine palaeoenvironments; problems associated with the isolation of calcareous nannofossils hampers their geochemical exploitation. However, geochemistry performed on calcareous nannofossil monotaxic assemblages should provide more meaningful data sets than those generated from the highly heterogeneous bulk carbonate. This protocol is based on cascade filtering steps, using polycarbonate membranes with well-calibrated pores. Strong ultrasonic treatment can further be applied to selectively reduce the size of particles for greater enrichment. Obtained residues frequently comprise near-monotaxic nannofossil assemblages. The application of this technique, which can be achieved within less than 2 days, has provided distinct fractions of coccoliths, calcareous dinoflagellate shells and also diagenetic monocrystals. This protocol is designed for application in reconstructing the history of water-column physicochemistry and diagenesis. It also has the potential to provide insights into the biogeochemistry of calcareous nannoplankton, including vital effects.