Wetland areas with varying amounts of emergent and free-floating vegetation may have very different microbial carbon and energy processing rates and and pathways. In Goose Lake Marsh, a natural prairie pothole wetland in central Iowa, transect measurements, continuous monitoring, and synoptic surveys were used to examine patterns light availability, temperature, dissolved O2 concentrations, dissolved CH4 concentrations, plant densities, litter densities, and CH4 flux due to diffusion and ebuliation within and outside emergent vegetation zones. Water column light availability was less than 2% of ambient light in emergent vegetated areas due to canopy cover, small floating plants (lemnids), and plant litter. Water temperatures and dissolved oxygen concentrations were significantly lower and varied less diurnally in vegetated areas. Photosynthesis and aerobic respiration rates in the water column were much greater in open water than emergent vegetation zones. CH4 concentrations in the water column were lower in open water than in emergent vegetation zones. But CH4 flux rates differences were not different due to increased plant cover and thicker stagnant boundary layers in the emergent zones which slow gas. Three habitat zones could be identified based on patterns in vegetation and dissolved oxygen: (1) a zone of dense emergent macrophytes providing significant submerged structure but with nearly or completely anoxic water, (2) a transition zone of sparse emergent macrophytes providing less structure but with more aerobic water, and (3) an open water zone with consistently aerobic water but with little submerged structure. A summary of the carbon budgets for the different zones indicates that the emergent zone was autotrophic while the open water and transitional zones were heterotrophic. Vegetation patterns are likely to control major aspects of wetland biogeochemistry and trophic dynamics. As a result, wetlands should be viewed as complex mosaics of habitats with distinct structural and functional characteristics.