The Everglades has been subjected to extensive anthropogenic alteration, mostly effecting ecosystem hydrology, over the past century. The original peat-accreting system stored large quantities of soil carbon (C) and was a sink for atmospheric CO₂. Hydrologic manipulation and wide-spread drainage have caused the oxidation, subsidence, and loss of large quantities of soil C. Understanding how Everglades tree islands soil respiration responds to water depth fluctuations coupled with organic matter (OM) production and soil accretion (C sequestration) can be used by managers to slow or reverse tree island loss. A conceptual empirically-based model for tree island soil C-budget was developed based on production and decomposition of OM as influenced by water depth fluctuations. Measurements were conducted in the Loxahatchee Impoundment Landscape Assessment (LILA) facility (Boynton Beach, Florida, USA), where macrocosms mimic Everglades ridge-and-slough and tree island landscape structure. Rates of C-input/output were balanced in LILA tree islands that varied by peat or limestone cores and water depths (elevation). Rates of C-input were estimated from litter production (OM), and rates of C-output from soil respiration (CO₂ efflux). Rates of subsidence were calculated as the difference between soil accretion and surface elevation change. Litter production, soil respiration, and soil accretion were higher at the higher elevations (drier) where trees are maximally productive. Surface elevation change (mean ± 1SE, -0.66 ± 0.22 cm yr^-1) was lower than vertical accretion (mean ± 1SE, 0.87 ± 0.10 cm yr^-1), predicting a subsidence of 1.53 cm yr^-1 in these young LILA tree islands. Both water depth and type of island core affected C-inputs/outputs. Carbon export resulted to be greater than inputs. This study helped to balance present-day C-inputs/outputs in the altered Everglades ecosystem; however a substantial portion of the C balance remains unaccounted for this experiment. Further research is needed to account for the contribution of belowground production to the total plant production and to determine the effect of live root respiration in order to improve our soil C-input/output estimates for restoration of Everglades tree islands.