Using hydrographic and zooplankton sampling along with stable isotope analyses, we determined the influence of freshwater input and of oceanic water ingress at the Golfo de Penas to the Baker Channel (47°S), central Patagonia, on the zooplankton community during mid-spring. Our results show that different taxonomic and functional groups occurred within the mesozooplankton community along an offshore-inshore-oriented transect. Some groups occurred mostly offshore (i.e. euphausiids, fish larvae, stomatopods, amphipods), while others occurred in higher abundance inshore (i.e. medusae, chaetognaths, siphonophores, ostracods). Early life stages of ecologically key species, such as Euphausia vallentini and pelagic stages of Munida gregaria, occurred mostly at the Golfo de Penas. Higher trophic positions estimated from δ15N occurred in mesozooplankton groups inshore (Baker Channel) and lower at the Golfo de Penas, coinciding with the decrease in C:N ratio in zooplankton and with an increase in chlorophyll-a values in the seawater seawards. The δ13C distribution in the zooplankton groups along the offshore-inshore transect showed a positive gradient from the inshore most stations towards the Baker Channel mouth, suggesting a negative relationship with freshwater carrying terrestrial organic carbon and a positive relationship with seawater. However, from the channel mouth seawards, a decrease in δ13C in most zooplankton groups occurred. Within the Baker Channel, low δ13C values occurred in particulate organic matter (POM) at the surface layer, higher values at intermediate depths, and low values at the deepest zones. This uneven distribution of δ13C values in POM and zooplankton, along with the presence of different water masses at different depths suggest an along-basin transport of organic carbon of different sources at different layers: of terrestrial origin at surface, marine origin at mid depth, and from degraded organic matter from offshore entering at higher depths. Thus, a complex scenario of lateral transport of water of different characteristics modulates the presence of zooplankton in different locations and their food sources along the area. These findings resemble others observed in further south in the Beagle Channel (57°S) also in spring but the relative contribution of different carbon sources may differ between Patagonian systems.