Abstract Conservation palaeobiology informs conservation and restoration of ecosystems by using the fossil record to discriminate between baseline and novel states and to assess ecosystem response to perturbations. Variability in the time-scale of palaeobiological data can generate patterns that either exaggerate or mute the magnitude of biotic changes. We identify two approaches that remedy the challenges associated with the mixing of baseline and post-impact states and with the transformation of the stratigraphic depth to time. First, combining surface death assemblages with both (1) fossil assemblages preserved in the subsurface historical layers and (2) living assemblages can better resolve the nature of ecosystem shifts than within-core surveys or live–dead analyses alone. Second, post-mortem age distributions of skeletal particles and their preservation states are not only informative about stratigraphic resolution and time averaging of death assemblages but also about the timing of changes in abundance of skeletal producers. High abundance of the youngest age cohorts in surface death assemblages is a null expectation of disintegration and burial dynamic. When this dynamic is accounted for, age distributions of benthic invertebrates from Holocene sediments often reveal high volatility, prolonged turn-offs in production or pervasive regime shifts that are obscured in the raw stratigraphic record.