Fjord and shelf food webs are frequently supplemented by the advection of external biomass, which in high-latitude seas often comes in the form of lipid-rich copepods that can support a wide range of fish species, including Northeast Arctic cod (Gadus morhua). A seasonal match or mismatch at the lower trophic levels (phytoplankton and zooplankton) is central in determining how much energy and biomass is available for higher trophic levels (fish). Here, we quantify the inflow of the copepod Calanus finmarchicus into the Vestfjorden fjord system using high-resolution measurements of ocean currents and zooplankton (laser optical plankton counter). We evaluate a spatio-temporal match/mismatch between the phytoplankton bloom and Calanus and assess the input of advected copeods at the lower trophic level fjord and shelf food web based on an integrative approach employing stable isotope analyses (C, N), fatty acid trophic marker analyses, and biovolume spectrum analyses. Our results suggest two different sources of the Calanus population in the fjord/shelf system: one fraction overwintered locally and started ascending early to feed on the phytoplankton bloom that peaked around April 11. The other fraction had only recently (end of April) been and still was being advected from the oceanic overwintering habitats. Ca. 119 g C/s of Calanus were advected into the fjord, comparable to the biomass of Calanus advected into an Arctic fjord, and the mesozooplankton community was dominated by the copepod. The fjord food web was tightly coupled between the phytoplankton spring bloom, the local part of the Calanus population (trophic level 1.8–2.4) and cod larvae (high levels of wax esters). On the shelf, our results suggest that the impact of advected Calanus in the food web is at its starting point (low trophic level, large difference of δ13C of POM and Calanus). We highlight important factors that can contribute to the successful spawning of Northeast Arctic cod: an extended phytoplankton bloom that can support both locally and advected Calanus, which in turn can supply the essential nauplii prey for first-feeding cod larvae.