In experimental wetland mesocosms located at Florida Bay Interagency Science Center, Key Largo, Florida, researchers continuously added salinity (approximately 6.9 g salt d-1) and phosphorus ( approximately 0.5 mg P d-1) to Cladium jamaicense peat monoliths from February 2015 to February 2017 and quantified changes in carbon partitioning. Several studies, focusing on the functional roles of marsh, soil, and microbe in the sawgrass-peat ecosystem, summarized detailed methodology and results (Wilson et al. 2019; Servais et al. 2019). Briefly, salinity was increased (~10 ppt) and phosphorus was added (0.45 mg P d-1) to simulate four treatment effects (n = 24 plots): i) freshwater and no-added phosphorus, ii) freshwater and added phosphorus, iii) saltwater and no-added phosphorus, and iv) saltwater and added phosphorus. Upon the termination of manipulation study (early February 2017), containers holding water and peat-sawgrass cores were drained, rinsed, and refilled with only freshwater without any added nutrient and salt. Then, we experimentally restored freshwater to previous treatment and control mesocosms from February 2017 to June 2018 to examine the capacity of wetland ecosystems to recover carbon losses from saltwater intrusion. Note that FCE1226_Water_quality.csv summarizes water quality during both the manipulation and restoration study; however, all other files in the Dataset Title section only summarize results from the restoration study. Detailed methodology is provided below.