Seagrass habitats are threatened by multiple anthropogenic stressors that adversely affect ecosystem structure and function, ultimately contributing to global declines in extent. Much of our current knowledge of multiple stressor impacts is derived from experiments that introduce stressors simultaneously and under static (constant) conditions without considering how natural environmental variability influences stressors. Most studies are also conducted in highly controlled laboratory experiments that do not account for abiotic and biotic processes that may affect stressor interactions and impacts. To address this critical knowledge gap, we investigated the in situ effects of more realistic introduction of multiple stressors within a seagrass community by incorporating changes in stressor intensity (i.e., fluctuations) and synchronicity (i.e., timing of fluctuations). Fluctuating stressors reduced seagrass shoot density and leaf surface area relative to static stressors. Static stressors increased seagrass leaf surface area and crustacean abundance. Additionally, stressor effects on crustaceans were mediated within the seagrass community. Our results suggest that experiments using static stressors could be underestimating detrimental stressor impacts, and thus have implications for how multiple stressor experiments should be conducted.