Wetlands are globally important biogeochemical hotspots, and their roles as either significant sources of greenhouse gas or carbon sinks are strongly controlled by environmental drivers such as carbon, nitrogen, and phosphorus availability, which can stimulate emission of three greenhouse gases: nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4). Mounting evidence suggests that aquatic invertebrate activity can enhance wetland greenhouse gas flux, through bioturbation and bioirrigation of surrounding sediments. However, waterbirds reduce the density of aquatic invertebrates, which could potentially reduce greenhouse gas flux. Alternatively, the nutrient contents of waterbird guano may stimulate microbial activity responsible for these gas fluxes. The research project FLAMMINGGOS (Functional Links in Avian, Microbial, Macrophyte, and INvertebrate Greenhouse Gas Output Stimulation) aims to test the relative strength of top-down and bottom-up effects of predatory waterbirds on wetland greenhouse gas fluxes. This study is a part of the FLAMMINGGOS project and studied the bottom-up stimuli effects of methane flux, through addition of waterbird guano to sediment cores sampled from three sites in Doñana, Spain. Guano did not enhance methane flux; on the contrary, the overall flux rates decreased after guano addition for one site. There was also a positive correlation between methane flux and the presence of benthic invertebrates. This suggests that the top-down gas-stimuli effects of waterbirds may be stronger than the bottom-up; benthivorous waterbirds, such as flamingos, may lessen the emissions of CH4 through predation on benthic invertebrates. Further research is however required to fully understand these interactions and gas flux stimuli effects.