A quantitative analysis of the depositional processes on the Mahakam Delta indicates that it is presently subsiding and is, in essence, a drowned delta that is being transgressed and modified by marine processes. Calculations of sediment transport rate indicate that most, if not all, fluvially derived sand is being stored onshore in the distributaries, whilst finer-grained sediment moves offshore. A fining-upward and increasingly marine-upward succession is being deposited in the distributaries, which is analogous to nearby outcropping and subsurface successions that have previously been interpreted as progradational.

The mixed fluvial and tide-dominant shoreline morphology is not solely a product of the deltas present-day processes. The fluvial component is a relict feature from a phase of progradation that preceded the ongoing transgression and is now being modified by tidal processes. Facies distribution is a much better indicator of modern depositional processes than delta morphology on the Mahakam Delta, suggesting that facies-based delta classifications are more accurate than morphology-based classifications. All the apparently anomalous components of the sedimentology and morphology are reconciled by a transgressive interpretation, including the overly deep distributaries, gently dipping subaqueous delta plain, penetration by benthic marine organisms far into the distributaries, widespread Nypa palm on the lower delta plain, and the long, mud-filled gap between sand in the distributaries and on offshore bars.

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