High winter respiration has been observed in a subarctic estuary with high levels of organic matter inputs, while winter is generally thought to be a non-productive season. We constructed an oxygen and carbon budget of the system to validate the high respiration rate, including the resulting low production-to-respiration ratio, and to identify important carbon and energy sources. Measurement data of production and respiration parameters from running monitoring programs were used. Furthermore, we set up a microcosm experiment in order to study effects of iron increases by riverine organic matter inputs. The carbon balance of this subarctic estuary shows a small deficiency of carbon on an annual basis, but is able to explain how winter respiration is fueled by carbon fixed in the autumnal season and inputs of riverine material. Also, the balance calculation was able to predict oxygen deficiencies on a seasonal basis. The effect of riverine organic matter on biological activity was clearly present, but iron did not appear to affect responses in primary or secondary producers. Additional studies will be needed to fully understand the role of iron additions to marine microbial communities, particularly focusing on fractioning of iron and organic matter species.