Abstract There is increasing evidence to suggest that drivers of bias in the fossil record have also affected actual biodiversity history, so that controls of artefact and true pattern are confounded. Here we examine the role of spatial structuring of the environment as one component of this common cause hypothesis. Our results are based on sampling standardized analyses of the post-Middle Eocene record of shelf molluscs from New Zealand. We find that spatial structuring of the environment directly influenced the quality of the fossil record. Contrary to our expectations, however, we find no evidence to suggest that spatial structuring of the environment was a strong or direct driver of taxic rates, net diversity, or spatial structuring in mollusc faunas at the scale of analysis. Stage-to-stage variation in sampling standardized diversity over the past 40 Ma exhibits two superficially independent dynamics: (a) changes in net diversity were associated primarily with changes in origination rate; and (b) an unknown common cause related extinction rate to the quality of the fossil record and, indirectly, to spatial structuring of the environment. We suggest that tectonic drivers, manifest as second-order sequence stratigraphic cycles, are likely to have been a key element of this common cause.