Typically, restoration goals target a point in history, i.e., pre-human influence state, however, ecosystems are dynamic and restoration goals must consider the potential evolution of the system, along with primary causes of landscape degradation and the resultant resilience. Using the Everglades as a case study, known disturbances were linked to biogeochemical and vegetation patterns to compare the divergence of the anthropogenically impacted landscape from that expected during natural peatland evolution. Specifically, landscape soil biogeochemistry of ~ 1100 sites was examined in context of hydroperiod, spatial and temporal trends in water quality from the 1940′s through present, elevation, and vegetation communities. This provided a link between carbon (C) accumulation and the influence of anthropogenic alterations. The network of canals created to manage water resulted in a greater ratio of surface water to rainfall contribution to the water budget, restored connectivity of groundwater to surface water, and facilitated overdrainage and mineral and nutrient enrichment of the ecosystem, causing multiple regime shifts and evidence of C loss. This study suggests that restoration can promote the accumulation of minerotrophic peats, but it is difficult to recreate the trajectory towards the ombrotrophic peatland, one of the end members and most C rich portions of the ecosystem, given changes in source waters and connectivity. In addition, a comparison with the literature and paleoecological data confirmed that while phosphorus (P) and C accumulation are positively related, even relatively small increases in P content reduced the proportional C content of peat soils. Overall, this study highlights the need to consider the potential natural trajectories of landscape development, the multiple coexisting resultant regimes, and the importance of soil biogeochemical properties when establishing and prioritizing restoration goals. Given the resilience and feedback loops of the anthropogenically impacted areas, active management of these areas may be necessary if we are to restore the vegetation community composition and biogeochemical characteristics to those of natural regimes, however, some legacy effects will constrain future restoration efforts.