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Although there have been extensive studies on the hydrological and erosional impacts of logging, relatively little is known about the impacts of conversion into agricultural plantation (namely rubber and oil palm). Furthermore, studies on morphological impacts, sediment-bound chemistry and forensic attribution of deposited sediment to their respective sources are scarcer. This chapter introduces the potential for using the multi-proxy sediment fingerprinting technique in this context. Featuring pilot projects in two major flood-prone river systems in Malaysia, the studies explore application of geochemistry-based sediment source ascription. The geochemical signatures of sediment mixtures on floodplains were compared to sediments from upstream source tributaries. The tributaries were hypothesised to have different geochemical signatures in response to dominant land management. The first case study took place in the Segama River system (4,023 km²) of Sabah, Malaysian Borneo where a mixture of primary forest, logged-forests and oil palm plantations were predominant. The second case study was in the Kelantan River Basin (13,100 km²) with two major tributaries (Galas River and Lebir River) where logged-forests and rubber and oil palm plantations are dominant land-uses. Both case studies demonstrated the applicability of this method in ascribing floodplain deposited sediment to their respective upstream sources. Preliminary results showed that trace elements associated with fertilisers (e.g. copper and vanadium) contribute to agricultural catchment signatures. Alkaline and alkaline-earth elements were linked to recently established oil palm plantations due to soil turnover. Mixing model outputs showed that contributions from smaller, more severely disturbed catchment are higher than those from larger but milder disturbed catchments. This method capitalises on flood events to counter its adverse impacts by identifying high-priority sediment source areas for efficient and effective management.