We examine the effects of natural and anthropogenic drivers on the functioning of benthic ecosystems using data including that from the inshore waters of Australia (SE Qld), Scottish fjords, the NW European shelf and the shallow coastal seas of the Jurassic. We make comparisons across decadal to millennial time scales. In all the systems analysed significant changes in the composition of the macrofaunal assemblage did not result in major changes in the ecological functioning of the system, as described by biological traits composition. However, in many of the systems considered high levels of perturbation were followed by a rapid collapse in functioning. The good news is that management measures to prevent further deterioration of our natural estate will ensure that ecosystem services will be maintained. The bad news is the confirmation of the, long hypothesised, tipping points in the functioning of marine ecosystems. This should prompt a more risk averse approach as considerations of the functional capacity risk being underestimated.