Fine sediment is a dynamic component of the fluvial system, contributing to the physical form, chemistry and ecological health of a river. It is important to understand rates and patterns of sediment delivery, transport and deposition. Sediment fingerprinting is a means of directly determining sediment sources via their geochemical properties, but it faces challenges in discriminating sources within larger catchments. In this research, sediment fingerprinting was applied to major river confluences in the Manawatu catchment as a broad-scale application to characterizing sub-catchment sediment contributions for a sedimentary catchment dominated by agriculture. Stepwise discriminant function analysis and principal component analysis of bulk geochemical concentrations and geochemical indicators were used to investigate sub-catchment geochemical signatures. Each confluence displayed a unique array of geochemical variables suited for discrimination. Geochemical variation in upstream sediment samples was likely a result of the varying geological source compositions. The Tiraumea sub-catchment provided the dominant signature at the major confluence with the Upper Manawatu and Mangatainoka sub-catchments. Subsequent downstream confluences are dominated by the upstream geochemical signatures from the main stem of Manawatu River. Variability in the downstream geochemical signature is likely due to incomplete mixing caused in part by channel configuration. Results from this exploratory investigation indicate that numerous geochemical elements have the ability to differentiate fine sediment sources using a broad-scale confluence-based approach and suggest there is enough geochemical variation throughout a large sedimentary catchment for a full sediment fingerprint model. Combining powerful statistical procedures with other geochemical analyses is critical to understanding the processes or spatial patterns responsible for sediment signature variation within this type of catchment. Copyright © 2015 John Wiley & Sons, Ltd.