Temperate Highland Peat Swamps on Sandstone (THPSS) are located at the headwaters of streams on low relief plateaus of Eastern Australia. Swamp sediment structure has a direct link to the high water tables, element cycling and carbon sequestration that are the characteristic functions of these systems. By comparing the sediment structure of intact swamps and channelised fills, we can gain an understanding of how changes in swamp geomorphology change both swamp structure and function. We examined the sedimentology of six intact and six channelised fill swamps in the Blue Mountains NSW, Australia. There were significant differences in texture, unit thickness, Carbon: Nitrogen (C:N) ratios and moisture content between intact swamps and channelised fills. The presence and thickness of unmodified contemporary sand layers in almost all channelised fills and its absence in almost all intact swamps was a distinctive structural difference. The two functional swamp layers, in terms of water and carbon storage were almost double the mean thickness in intact swamps than in channelised fills. Moisture content was 30% higher in intact swamps than in channelised fills. Mean C: N ratios for channelised fills were 25% lower than that of intact swamps. Peat forming potential, as defined by C:N ratios > 27, started at a greater depth in the sediment profile (0.9 m lower) in channelised fills than in intact swamps. It is clear from this study that these structural and functional indicators are important for assessing swamp condition and can also be useful in designing monitoring programs for management and rehabilitation that target key structural attributes that produce and maintain swamp function.