Spatial heterogeneity in ecosystem metabolism may play a critical role in determining ecosystem functions. Variation in ecosystem metabolism between macrophyte patches in shallow wetlands at the extremes of freshwater habitats has not been investigated. We estimated ecosystem metabolism in mesocosms containing different macrophytes using 24-hour oxygen curves to test our hypotheses: (1) net aquatic production (NAP) during spring and summer would be similar among algal patches (metaphyton and Chara), (2) NAP in algal patches would be greater than patches dominated by the vascular plant Potamogeton foliosus, (3) heterotrophy and anaerobiosis would be greatest in patches dominated by Lemna, and (4) the pond would be autotrophic in the spring and fall but heterotrophic in the summer. We found that different patches generated differences in NAP but not always as we predicted. NAP was different among algal patches in the spring and summer, and only metaphyton was more heterotrophic than P. foliosus. In the summer Chara and Lemna patches were heterotrophic and metaphyton became autotrophic. As predicted, the pond was net autotrophic in the spring and heterotrophic in the summer with an absence of patchiness in fall attributed to the dominance of Lemna. This research suggests the importance of macrophyte patchiness in wetlands in determining patterns of ecosystem metabolism despite challenges in measuring 24 hour oxygen curves (e.g. oxygen supersaturation). Consequently, macrophyte traits may be important in determining spatial heterogeneity of ecosystem metabolism in shallow ponds.