Ecosystem resilience to pressures expanding and contracting within the adaptive cycle as slow variables change. However, little is known about their role in defining reference conditions for wetland restoration. Here, we applied paleoecological data of two wetlands that have been degraded (Honghe, riparian peatland) and disappeared (Shenjiadian, valley peatland) to evaluate ecosystem resilience to anthropogenic pressures as the phases of the adaptive cycle progress. The slow variables of plants and diatoms gradually began to change from moisture to dry loving species under severe disturbances in the late 1970s. Then regime shift took place around 1990 CE (Current Era) based on a sequential T‐test analysis and F statistics on the slow variables. A drop in water level caused by human activities rather than climate moisture led to regime shifts in Honghe and Shenjiadian wetlands. Therefore, the ecosystem were in the conservation phase before the late 1970s, and were in the reorganization phase after 1990 CE. The ecosystems had high resilience and a stable state at the early conservation phase, and its characteristics can be used as reference conditions for wetland restoration. The reference water level was 11–13 cm and the NH4‐N ranged from 0.8 to 1.2 mg/L. The dominant vegetation was Drepanocladus aduncus and the dominant diatom was Pinnularia brevicostata. The referred enrich factors of nitrogen, phosphorus, and heavy metals were under 4.45, 2.12, and 1.11, respectively. Considering both adaptive cycle and resilience to define reference conditions can provide insight into the future restoration and management of wetland ecosystems worldwide.