Cores obtained from a coastal freshwater lake (Lake Waihola, South Island, New Zealand) show a >4000year history of environmental changes driven by significant variations in marine influence and anthropogenic modification of the catchment and minor contributions such as possible palaeotsunami inundation, all taking place against a background of sea level and landscape change. A marked shift from estuarine conditions (salinity >14ppt) to a predominantly freshwater state occurred around the mid-Holocene. This shift is recorded as a distinct change in diatom assemblages and by the disappearance of the estuarine bivalve Austrovenus stutchburyi from the sedimentary record. More recently, a marked change in sediment characteristics and changes in the pollen record correlate with rapid anthropogenic land clearance and conversion of the catchment to intensive agriculture in the mid 1800's. The mean rate of sediment accumulation between c. 4000yr BP and the start of major European settlement (c. AD1860) were around 0.18±0.01mmyr−1. From c. AD1860 onwards, this has increased markedly by about 30 fold following major land use changes in the catchment. Based on current predictions of sea level rise and sediment accumulation, various future sea level rise scenarios will more than compensate for infilling, resulting in the persistence of this aquatic system, which is expected to revert to an estuarine state.