From University of Texas at Austin Marine Science Institute to Texas Water Development BoardInteragency cooperative contract TWDB contract no. IA03-483-003July 2004Ecosystem function in estuarine environments is known to be an important indicator of ecosystem health and productivity. There is a need to quantify estuarine ecosystem function variability and link to freshwater inflow to enable better management of ecosystem health and productivity. An important and quantifiable component of ecosystem function is ecosystem metabolism. Results indicate that open water methods were more appropriate than light-dark bottle methods for measuring net ecosystem metabolism in shallow water estuarine ecosystems because of the large contribution of benthos, which is ignored in water bottles. Spatial and temporal variability in net ecosystem metabolism was found. Spatial variability was attributed to differences in benthic habitats and/or station locations with respect to freshwater inflow point sources. Temporal variability in net ecosystem metabolism may be driven by differences in seasonal temperatures and freshwater inflow differences on seasonal time scales. Net ecosystem metabolism was directly related to amounts of freshwater inflow. The strength of this relationship depended on proximity to freshwater sources. Future studies of whole ecosystem metabolism in shallow estuarine ecosystems should employ open water methods and should strive to link other dynamic environmental conditions, such as temperature or irradiance, to ecosystem health, function, and productivity.Marine Scienc