Macroscopic ecosystem studies often complete our knowledge based on population-level experiments and models. In this paper, the changed control of ecosystem functioning is reported by analyzing the structure of the energy flow network of a tidal marsh community (Crystal River, Florida). The positional importance of trophic components is characterized by a graph theoretical approach. Then, positional importance of points is compared to the magnitude of fitting carbon flows (i.e., the importance of links) and the congruency is expressed in percents. These results are presented for both an unperturbed (control) and a thermally stressed creek ecosystem of the river. The comparison of average congruency values for the two communities suggests that, first, trophic control may be stronger in the stressed community and, second, the reliability of carbon flows is also higher in the stressed ecosystem.