Foraminiferal assemblages preserved in estuarine sedimentary sequences along the coast of South Otago, New Zealand, provide evidence for three Holocene fault-displacements and associated earthquakes within the 250 km-wide continental collision zone along the Australian-Pacific plate boundary. The modern analogue technique was used to estimate paleotidal elevations of the fossil foraminiferal faunas, based on an analogue set of 334 modern New Zealand faunas (including data from three new intertidal transects taken from the studied estuaries). These elevation estimates provide a record of abrupt changes in tidal elevation, which are inferred to have been produced by vertical displacements on nearby faults. The foraminiferal record in cores (0.75–2.8 m long) from Akatore Estuary identify the previously recognized last rupture (~1100 cal yrs BP) on the Akatore Fault, with ~0.4 m of subsidence on the western side produced by actual downthrow or shaking-related compaction of underlying sediment. The foraminiferal record in cores (1.4–7.0 m long) and in an uplifted terrace section from tidal Catlins Lake provides the first evidence of Holocene fault rupture and major earthquake risk south of the Clutha River mouth. Three displacement events on the Settlement Fault, which forms the eastern margin of Catlins Lake, are recognized. The youngest (~1000 cal yrs BP) resulted in 0.4 m of subsidence (downthrow or compaction) on its west side. The penultimate (~3600 cal yrs BP) resulted in ~1.2 m of uplift of an extensive terrace on the east side of the fault with consequent narrowing of the estuarine entrance and reduced salinity in the tidal lake (recorded by foraminiferal faunas). The earliest event (~5000–4500 cal yrs BP) is recognized by ~1 m of abrupt subsidence on the west (Catlins Lake) side of the fault. Foraminiferal faunas in the upper parts of the majority of cores (from high tidal salt meadows) also document ~0.3 m of sea-level rise within the last 150 years.