Microbial methanogenesis within surface aquatic systems mainly occurs in bottom anoxic sediments, where fresh organic matter accumulates from litterfall, dead plant materials and root exudates, e.g., [18; 19], although CH\({}_{4}\) production was also observed under aerobic conditions, e.g., [20; 21; 22; 23; 24]. Once released from bottom sediments, CH\({}_{4}\) can upwardly move through the water column and reach the atmosphere via different pathways, including molecular diffusion, ebullition and storage flux, e.g., [25]. The latter occurs under peculiar conditions, being referred to the sudden release of CH\({}_{4}\) either accumulated due to water stratification or trapped by ice formation. Methane ebullition consists in the release of gas bubbles from bottom sediments to the atmosphere with negligible physical, chemical or biological interactions, and, although relevant, it is an intermittent phenomenon. On the other hand, diffusive flux is responsible for the continuous release of a large portion of CH\({}_{4}\) at the water-atmosphere interface and it is the most commonly estimated component of the total flux from surface waters, e.g., [17] and references therein. The diffusive flux is strictly related to the capability of CH\({}_{4}\) released from bottom anoxic sediments to escape oxidation within the water column and, hence, it largely depends on both lake characteristics (e.g., surface area, water depth, mixing regime and trophic state) and external drivers (e.g., temperature, precipitation and landscape), e.g., [25] and references therein [26]. Accordingly, dissolved CH\({}_{4}\) concentrations can be highly variable in both time and space even within a single surface aquatic system, e.g., [27], making estimates of global CH\({}_{4}\) emissions from these ecosystems difficult to be evaluated. Methane emissions from aquatic ecosystems are mainly estimated by direct or indirect measurements of diffusive fluxes from open waters, e.g., [25]. Nevertheless, recent studies have highlighted the importance of macrophytes in regulating CH\({}_{4}\) emissions from wetlands, although their influence in promoting or hindering methanogenesis is debated, e.g., [28; 29; 30; 31; 32]. In particular, _Phragmites australis_ (common need) was suggested to be particularly effective in transporting gas from the submerged soil to the atmosphere and accreting large amounts of carbon substrates to methanogens enhancing CH\({}_{4}\) production, e.g., [33] and references therein [34; 35]. Hence, several knowledge gaps still subsist on how environmental drivers regulate CH\({}_{4}\) emissions from aquatic ecosystems, limiting upscaled efforts to estimate global emissions from surface aquatic systems [36]. Available studies limited to a relatively small number of waterbodies likely produce an underestimation of the global variability in CH\({}_{4}\) emissions, whereas limited data on spatial and temporal variability in CH\({}_{4}\) emissions within single aquatic systems may induce uncertainty on global emissions based on open-water flux values [36] and references therein. In this paper, we present data on CH\({}_{4}\) diffusive fluxes from two wetlands located in the Versilian Plain (northern Tuscany, Italy), i.e., Porta and Massaciuccoli Lakes. The former is a shallow wetland largely invaded by reeds, which are currently experiencing a progressive decline, and raising annoyances in ambient air quality because of odor problems related to biogenic H\({}_{2}\)S emissions from the lake surface [37]. Massaciuccoli Lake has a surface of ca. 700 ha with a wide surrounding marsh interconnected with the sea and is located in a highly anthropized region consisting of both urban and rural areas. Accordingly, these two diverse wetlands, located within the same geographic and climatic zone, offer the opportunity to investigate the physicochemical environmental drivers shaping the spatial and temporal variability of CH\({}_{4}\) diffusive fluxes within each single system.