Environmental perturbations are ubiquitous features of ecosystems and shape ecological structure and function. Climate change will alter the intensity and frequency of disturbances and expose ecosystems to novel combinations of useful inputs (subsidies) and harmful inputs (stressors). Coastal wetlands are particularly vulnerable to changing environmental conditions and are increasingly exposed to effects of interacting subsidies and stressors. In particular, the Florida Coastal Everglades, which has experienced accelerated change due to a history of water management practices, is vulnerable to new disturbances associated with climate change. The low-lying Florida Everglades faces multiple disturbances from storm surge, nutrient enrichment, and sea-level rise which will influence its responses to future environmental perturbations. Microbial communities are often used to characterize environmental change because of their high surface area to volume ratio, permeable membrane, and quick turnover rates. Therefore, assessing how microbial function changes can provide insights into how subsidies and stressors interact to alter biogeochemical cycles. I tested how nutrient enrichment can alter ecosystem responses to stress and found that it did not promote recovery in mangrove plants. I examined how long-term exposure to salinity and phosphorus (the limiting nutrient in the Everglades) affected microbial enzyme activity and found that salinity alone acts as a suppressor of enzyme activity but phosphorus addition can mitigate salinity stress in sawgrass soil. I tested how pulses of salinity can affect the microbially-mediated breakdown of organic material and found that the microbial community was functionally redundant and unaffected by saltwater pulses; however, microbial activity was consistently lower in the brackish marsh compared to the freshwater marsh. I investigated how gradients of salinity and phosphorus affected freshwater and brackish soils and determined previous exposure to saltwater intrusion dominates affects microbial function and soil composition. Across these experiments, I found that environmental perturbations alter the microbial-mediated processing of nutrients and carbon, and legacies of previous disturbances influence the microbial response to new disturbance regimes.