Reconstructing the provenance of siliciclastic marine sediment is important for understanding sediment pathways and constraining palaeoclimate and erosion records. However, physical fractionation of different size fractions can occur during sediment transport, potentially biasing records derived from bulk sediment. In this study, records of radiogenic Sr and Nd isotopic composition and K/Al ratio of the separated clay fraction, as well as bulk grain size, are presented, measured from deep-sea sediments recovered from International Ocean Discovery Program (IODP) Sites U1456 and U1457 in the Arabian Sea. These new records are compared with published bulk sediment records to investigate the influence of sediment transport on these proxies and to constrain provenance evolution and its relationship to climate variability since middle Miocene time. Correlations between grain size and the bulk sediment isotopic composition confirm that transport processes are influencing the bulk sediment record. This relationship, although present, is not as strong in the clay-fraction isotopic records. Heterogeneity of bulk sediment likely drives differences between bulk and clay records, thought to be largely controlled by sediment transport processes. The isotopic records reveal variations in provenance that correlate with climatic change at 8–7 Ma, as well as an increase in overall provenance variability beginning at c. 3.5 Ma, likely linked to monsoon strength and glacial–interglacial cycles. The clay-fraction records highlight the potential value of measuring proxy records from multiple size fractions to help constrain provenance records as well as investigate sediment transport and/or weathering and erosion processes recorded in deep-sea sediment archives.