Shallow coastal zones are intensely used by humans but simultaneously are biodiversity hotspots, with a crucial role in the life cycle of many marine species. The competition for food or space between humans and protected wildlife intensifies under pressure of an increased need for marine resources for human consumption. For successful management it is important to establish the key components driving such conflicts of interest. Here we focus on the protected common scoter (Melanitta nigra), a sea duck wintering in coastal habitats that are rich in food, but also among the most disturbed marine systems worldwide. Due to the scoters' shyness disturbance impacts the birds’ ability to forage and poses a conflict for balancing bird conservation and economics, including a fishery on its main bivalve prey Spisula subtruncata. In this study, we use an energy budget model to quantify the consequences of depth, currents and disturbance on scoter energetics and carrying capacity. Energetics were described using physical parameters and field data on food availability and disturbance. Results reveal non-linear relationships and a threshold value for when a scoter can no longer maintain its energy balance. This is caused by limited foraging time, rather than food availability. From a conservation perspective, this implies that a precautionary principle should be used, because there will be no warning when an area becomes unsuitable. In addition, the model was applied to study the effects of disturbance from different kinds of shipping in a coastal area of the North Sea, north of The Netherlands. Cargo shipping has the largest impact on the carrying capacity, where there is spatial overlap of prey and an intensively used shipping lane. In other prey distribution situations shrimp vessels may cause most disturbance. Spisula-Ensis fisheries did not limit the potential carrying capacity due to the limited catches and number of fishing trips. Scoter protection should be aimed at flexible spatial management and on only those vessel types above a Spisula bed with a large number of trips, and above all should work from a precautionary principle given the critical thresholds for scoter presence.