The concentrations of ambient nutrients and dissolved organic carbon (DOC) in northern coastal ecosystems often show large variations, due to the spatiotemporal differences in terrestrial inputs. How these variations affect the stoichiometry of coastal planktonic organisms is, however, poorly known. Here we assessed the spatiotemporal variability of C, nitrogen (N), and phosphorous (P) concentrations of the seawater on the elemental stoichiometry of seston and dominant mesozooplankton taxa in a coastal area of the northern Baltic Sea. The freshwater inflow peaked in spring following the snowmelt and brought a significant amount of DOC, but not N and P to the coastal system. DOC was the main environmental descriptor for seston C:N stoichiometry. The C:N ratio of seston from 0.7 to 50 μm and mesozooplankton followed the temporal pattern of water C:N ratio, while the temporal trend of bacteria C:N showed an opposite pattern. Our results also indicated that the C:N ratio of seawater controlled both seston and mesozooplankton C:N ratios. Our findings imply that inflows of terrestrial DOC alter the stoichiometry and reduce the nutritional quality of planktonic food webs in northern coastal ecosystems.