Previous studies suggest that anthropogenic warming has affected the multi-decadal trend patterns of sea level over the Indian Ocean (IO). This effect, however, has not been quantified. Using observational datasets combined with large ensemble experiments from two climate models, this paper assesses the effects of natural internal variability versus external forcing on the observed, multi-decadal trend pattern and the decadal sea level anomaly (SLA) of the IO since the 1960s. Because the global mean sea level rise (SLR), which results largely from external forcing, has been removed before the examination, the paper focuses on the regionally uneven distribution of trend and SLA. The impacts of climate modes are quantified using a Bayesian Dynamic Linear Model. For the regional trend pattern of 1958–2005, the effects of internal variability dominate external forcing. Over the Seychelles area where sea-level variations obtain the maximum, internal variability (external forcing) contributes 81% (19±2.4%) of the observed trend. For decadal SLA, internal variability is the predominant cause, with a standard deviation (STD) ratio of externally forced/observed SLA being 18±17% over Seychelles and 17±11% near the Indonesian Throughflow (ITF) area. Climate modes account for most observed SLA during boreal winter, with the total effects of decadal ENSO, Indian Ocean Dipole (IOD), and monsoon accounting for 78–86% of the observed STD near the Seychelles region, ITF area, and coasts of Sumatra and the Bay of Bengal. During summer, climate modes explain 95% of observed STD near the ITF but only 58–67% in other regions. Decadal ENSO dominates the SLA in the south tropical IO for both seasons and near the coasts of Sumatra and the Bay during winter. Decadal IOD and monsoon, however, control the coastal SLA during summer. Remote and local winds over the IO are the main drivers for decadal SLA, while the Pacific influence via the ITF is strong mainly in the southeast basin.