The flow and balance of dissolved inorganic nitrogen and dissolved inorganic phosphorus in Seno Gallegos (Cordillera Darwin) was estimated for the first time. In addition, the response of these processes was evaluated under two rainfall conditions, one above and one below the local historical average. To estimate the flow and balance of nutrients, a LOICZ model of double layers was used. Primary data on nitrogen and phosphorus concentration were obtained from water samples, which were collected during fall, winter, and spring 2010 in Seno Gallegos. In the surface layer of the Seno Gallegos the balance of dissolved inorganic nitrogen showed a consumption and output of nutrients. While the vertical flow is predominantly from the deep layer to the surface one. The phosphorus balance of the Seno Gallegos was negative for the upper layer and positive in the deep layer. Under a condition of increased rainfall, nutrient balance and flow would be intensified, along with increased nitrogen fixation and net metabolism. While under a condition of lower rainfall, these processes would be diminished. Due to the direct relationship between variations of the glacial ice volume and its adjacent proglacial marine area, the latter are highly sensitive to climate change. Therefore, further studies on these areas are of great importance to understand the forces that govern these cold estuarine ecosystems.