Floodplain wetland ecosystems respond dynamically to flooding, fire and geomorphological processes. We employed a combined geomorphological and environmental proxy approach to assess allochthonous and autochthonous macro-charcoal accumulation in the Macquarie Marshes, Australia, with implications for the reconstruction of fire regimes and environmental conditions in large, open-system wetlands. After accounting for fluvial macro-charcoal flux (1.05 ± 0.32 no. cm-2 a-1), autochthonous macro-charcoal in ~1 m deep sediment profiles spanning ~1.7 ka were highly variable and inconsistent between cores and wetlands (concentrations from 0 to 438 no. cm-3, mean accumulation rates from 0 to 3.86 no. cm-2 a-1). A positive correlation existed between the number of recent fires, satellite-observed ignition points, and macro-charcoal concentrations at the surface of the wetlands. Sedimentology, geochemistry, and carbon stable isotopes (δ13C range -15 to -25 ‰) were similar in all cores from both wetlands and varied little with depth. Application of macro-charcoal and other environmental proxy techniques is inherently difficult in large, dynamic wetland systems due to variations in charcoal sources, sediment and charcoal deposition rates, and taphonomic processes. Major problems facing fire history reconstruction using macro-charcoal records in these wetlands include: (1) spatial and temporal variations in fire activity and ash and charcoal products within the wetlands, (2) variations in allochthonous inputs of charcoal from upstream sources, (3) tendency for geomorphic dynamism to affect flow dispersal and sediment and charcoal accumulation, and (4) propensity for post-depositional modification and/or destruction of macro-charcoal by flooding and taphonomic processes. Recognition of complex fire-climate-hydrology-vegetation interactions is essential. High-resolution, multifaceted approaches with reliable geochronologies are required to assess spatial and temporal patterns of fire and to reconstruct in order to interpret wetland fire regimes.