The aggregation of plankton species along fjords can be linked to physical properties and processes such as stratification, turbulence and oxygen concentration. The goal of this study is to determine how water column properties and turbulent mixing affect the horizontal and vertical distributions of macrozooplankton along the only northern Patagonian fjord known to date, where hypoxic conditions occur in the water column. Acoustic Doppler current profiler moorings, scientific echo-sounder transects and in situ plankton abundance measurements were used to study macrozooplankton assemblages and migration patterns along Puyuhuapi Fjord and Jacaf Channel in Chilean Patagonia. The dissipation of turbulent kinetic energy was quantified through vertical microstructure profiles collected throughout time in areas with high macrozooplankton concentrations. The acoustic records and in situ macrozooplankton data revealed diel vertical migrations (DVM) of siphonophores, chaetognaths and euphausiids. In particular, a dense biological backscattering layer was observed along Puyuhuapi Fjord between the surface and the top of the hypoxic boundary layer (∼ 100m), which limited the vertical distribution of most macrozooplankton and their DVM, generating a significant reduction of habitat. Aggregations of macrozooplankton and fishes were most abundant around a submarine sill in Jacaf Channel. In this location macrozooplankton were distributed throughout the water column (0 to ∼ 200m), with no evidence of a hypoxic boundary due to the intense mixing near the sill. In particular, turbulence measurements taken near the sill indicated high dissipation rates of turbulent kinetic energy (ϵ ∼ 10-5Wkg-1) and vertical diapycnal eddy diffusivity (Kρ∼ 10-3m2s-1). The elevated vertical mixing ensures that the water column is well oxygenated (3-6mLL-1, 60%-80% saturation), creating a suitable environment for macrozooplankton and fish aggregations. Turbulence induced by tidal flow over the sill apparently enhances the interchange of nutrients and oxygen concentrations with the surface layer, creating a productive environment for many marine species, where the prey-predator relationship might be favored.