Abstract Bivalve shells from shelf and slope environments of the Benguela upwelling system were examined for their state of preservation for the first time, and were used to test whether their preservation is a proxy for spatially variable seafloor taphonomic conditions that lead to different degrees of time averaging. Distinctive shell damage-profiles show increasing shell damage further from the centre of the upwelling cells affected by anoxic conditions (opal and organic-rich) and towards the carbonate- and phosphate-rich facies (with slower sedimentation rates at the margins of the cells. Discrete taphofacies range from a very low damage profile (opal and organic-rich, facies 1) to very high damage (phosphate, facies 3), with elevated numbers of rounded, fragmented and bored shells as well as very little associated sedimentary matrix. This gradient in taphofacies is associated with a gradient from census assemblages with low damage to (within-habitat time-averaged) assemblages in carbonate and (environmentally-condensed) phosphate facies of moderate and higher species richness that are associated with increasing time averaging. This pattern follows the upwelling facies gradient of high opal and organic matter in areas of most intense upwelling cells and outward to aerated but food-abundant carbonate-rich seafloors and spatially coexisting phosphorite-rich concentrations. Thus, the taphonomic gradient ranges from stressful, oxygen-depleted seafloor environment under upwelling regimes that limit metazoan predators and borers (and thus minimize destruction), to well-oxygenated seafloors with increased predators and micro-boring animals that all foster post-mortem shell destruction. The rarity of encrusters is a conspicuous feature of these facies across the whole gradient that may reflect temporary recurrence of oxygen-depleting conditions even at the carbonatic and phosphatic facies. The state of preservation of these shells can serve as a modern analogue for identifying similar settings in the geological record but also for Anthropocene settings affected by eutrophication and expanding oxygen minimum zones. Molluscan taphofacies with unusually low levels of skeletal damage from borers and encrusters can thus represent sensitive proxies of conditions affected by Anthropocene deoxygenation and eutrophication.