The Manutahi-1 core of Wanganui Basin, New Zealand, provides a special opportunity to investigate variations in depositional paleoenvironments by way of high-resolution paleoecologic and sedimentologic studies in a succession that accumulated under the influence of late Neogene rapid glacioeustatic sea-level oscillations. Thirty cyclothems of the Matemateaonga Formation (late Miocene–early Pliocene) have been identified through a 960 m interval of the core. Temporal patterns in both lithofacies distribution and macrofaunal paleoecology indicate a close link with environmental shifts that took place over the duration of these sixth-order sea-level cycles (∼41 kyr duration). Because foraminiferal assemblages have proven to be depauperate in the Manutahi-1 core, macrofossils, especially bivalves and gastropods, are used as the primary source of paleoecologic data. The paleoenvironmental analyses presented here have relied extensively on the transfer of ecologic data from the modern fauna to extant or closely related species observed in the core. Most notably, a relative sea-level curve has been constructed for the Matemateaonga Formation from analysis of bathymetric data for appropriate modern taxa. A range of exploratory statistical approaches, including cluster and ordination techniques, allow rapid, objective, and reproducible classification of macrofaunal associations and the elucidation of large-scale paleoenvironmental patterns. Several implications arise from this study. First, sequence boundaries and other key surfaces are confidently identified on the basis of integrated sedimentologic, taphonomic, and paleoecologic investigation. Second, changes in depositional environment and the responses of benthic communities are revealed at a range of temporal scales. The temporal pattern of paleoecologic change appears to be the result of lateral, facies-related shifting of biofacies (habitat tracking) in response to sea level, sediment flux, and other associated paleoenvironmental variables. Temporal patterns of biofacies occurrence and diversity are, however, strongly overprinted by stratigraphic and taphonomic processes.