A major challenge to ecologists is identifying factors that make a system susceptible to regime shifts or state transitions. Theory and modelling have suggested a number of indicators to warn of approaching tipping points, but empirical tests of their validity are few. We tested 2 indicators, change to a key species and increased temporal variability, in a harbour, a system type rarely studied for regime shifts and alternate states. Long-term monitoring over 20 yr on a number of intertidal sandflats allowed us to document change and determine potential contributing factors. We detected decreasing abundance in the key species and increased temporal variability ( flickering) of community composition before a trophic and functional change to an alternate community type. Detection of these indicators occurred despite cyclic patterns in community and population dynamics and a relatively fast and permanent change of one external condition ( nutrients). We provide evidence that this shift was the product of a relatively small change in management of sewage disposal, combined with climate dynamics and mediated through changes in a key species, a tubeworm that provides biogenic habitat structure, stabilises sediment and affects dispersal and recruitment. These factors all interacted to escalate the effect of the relatively small changes in nutrients across a tipping point.