We investigated the response of nutrient cycling in the Lower St. Lawrence Estuary (LSLE) to perturbations, using a linear three-box model that reflects summer stratification. The model is used to (i) test the sensitivity of each layer’s nutrient concentration (fixed-nitrogen, phosphorus, and silica) to perturbations in nutrient and water volume inputs to the LSLE, (ii) compute the response time of the system to a new steady state following a perturbation, and (iii) estimate the amount of oxygen consumed by respiration as bottom waters are advected through the LSLE. We find that the system adjusts rapidly to perturbations (half a year to reach 90% of the new steady state under a doubling of river input nutrient concentration). Most of the dissolved nutrients (60% of the fixed-nitrogen, 85% of the soluble reactive phosphate) that reach the surface waters in the LSLE originate from deeper waters. This dampens the effect of nutrients of anthropogenic origin on eutrophication (a doubling of river input nutrient concentration will lead to less than a doubling of bottom-water respiration rates). Our nutrient budget suggests that the Lower St. Lawrence Estuary acts as a nutrient pump for the Gulf of St. Lawrence and nitrate appears to be the limiting nutrient to surface productivity in the LSLE. This model can be used to test the impact of natural or anthropogenic perturbations on nutrient in the LSLE and oxygen concentrations in its bottom waters. •We present a box model of nutrient cycling in the Lower St. Lawrence Estuary (LSLE).•We test the impact of natural or anthropogenic perturbations on nutrients and oxygen.•50% riverine and 25% deep concentrations increase result in 30% more eutrophication.•The effect of nutrients of anthropogenic origin is dampened by upwelling.•The Lower St. Lawrence Estuary (LSLE) adjusts rapidly to perturbations.