The depletion of dissolved oxygen (DO) in global oceans is a growing concern. This phenomenon is observed in coastal and oceanic waters, where different mechanisms contribute. In the Estuary and Gulf of Saint Lawrence (SL), this process of deoxygenation has been documented and is mainly attributed to a greater inflow of the warm, DO-poor North American Central Waters deeper in the water column, isolated by a persistent pycnocline. The responses of organisms chronically under these conditions, particularly benthic invertebrates with low to no mobility, usually encompass molecular modifications (thus complex physiological changes), to cope with environmental hypoxia. Such changes might also be reflected on the proteome, given the range of functions of these molecules on cell structure and metabolism. However, the characterisation of complex proteomic responses in situ is not yet fully addressed. Therefore, the aim of this work is to describe and compare the proteomic profile of a benthic invertebrate across the natural deoxygenation gradient of the SL. We sampled individuals of the annelid Neloeanira tetragona from four subregions across the gradient of the SL and on a well oxygenated outgroup region, the Saguenay Fjord. Proteins were identified and quantified by high resolution LC-MS/MS on whole body samples. The profiles obtained were tested both via pairwise comparisons and multivariate modelling using environmental data. These analyses ultimately highlighted site-specific responses, particularly linked to DO levels, with an overrepresentation of energy metabolism, cell signalling and protein homeostasis pathways. N. tetragona exhibits a compensatory accumulation strategy to cope with environmental chronic hypoxia.