The microfossils in eight short sediment cores in Mahurangi Harbour, northern New Zealand, record major ecological changes since colonisation by Europeans. During the period of catchment deforestation (1850s–1900) these changes include increased sedimentation rates, decline of soft-shore molluscs, increased diatoms and seaward migration of brackish, agglutinate-dominated, foraminiferal associations, inferred to be due to increased freshwater runoff and decreased pH. The interval of most rapid change (1950s–1980s) occurred before and during the establishment of oyster farms, which therefore are not implicated. Comparison of the microfossil content of surface sediment samples taken inside and outside of four oyster farms indicates variable effects dependent on farm location. In less saline sites, the presence of oyster-shell debris in sediment beneath oyster farms appears to have buffered the foraminiferal faunas from some of the impacts of lowered salinity and pH. At more tidally flushed, saline sites, the oyster farms influence a wider surrounding area that has lower relative abundance of three species of Elphidium and other calcareous Foraminifera, attributed to slightly muddier sediment, higher nutrients and consequently lower oxygen. A newly arrived exotic foraminifer, Elphidium vellai, appears to be an indicator species for the enhanced nutrient, carbonate-rich conditions beneath oyster farms.