Methane emissions from freshwater, mineral-soil wetlands represent an important portion of the global greenhouse gas budgets. We use long-term observations in Old Woman Creek (OWC), an estuarine wetland at the coast of Lake Erie. OWC is characterized by a fluctuating water level controlled by a natural sand barrier. OWC water levels are high when the barrier is closed. When it breaks, OWC is directly connected to the lake. Long term water level rise of Lake Erie provides a trend of water level at OWC. These changes to hydrology drive changes to the ecology. In OWC the dominant eco-hydrological patch types are mudflats, cattails (Typha), floating-leaf vegetation (Lotus, water lily), and open water. The seasonal and long term changes to water level lead to dynamic changes in the patch type composition, and as OWC gets deeper, mudflats and cattails give way to open water and floating-leaf vegetation. We developed an approach to classify the eco-hydrological patch type from remote sensing images. We used seasonal time series of NDVI from HLS (a composite dataset of Sentinel and Landsat). These time series were classified to patch types according to their similarity to the seasonal NDVI profiles of pixels identified and ground-truthed as pure pixels of a specific patch type. We then used the DG-SWEM high resolution hydrodynamic model to simulate the flow velocity throughout the wetland. Combining the eco-hydrological patch locations and the high-resolution flow simulation allowed for the calculation of an effective patch-type-level residence time. We found differences in residence times between the different patch types. We measured the relations between methane flux and CO₂ uptake at the whole wetland scale, the vegetation patch scale, and directly from leaves. We found different methane-CO₂ relations among the floating leaved and emergent species. Phenological transitions throughout the growing season continued to make an important effect only in Typha. Our observations represent a valuable foundation towards a more robust models of methane fluxes in wetlands at the resolution of within-wetland vegetation patch type, and resolving the effects of seasonal and within-season vegetation phenology in ecosystem-scale models.