The study area encompasses the Puyuhuapi fjord (300 m depth) and Jacaf channel (200-400 m depth), located at ∼44° S in Patagonia. The Puyuhuapi fjord is connected to the open ocean by two mouths, where at one mouth, a shallow sill inhibits ventilation of deep fjord water. This study is aimed to improve our understanding of the zooplankton distribution and migration patterns in the Puyuhuapi fjord and Jacaf Channel. To accomplish this, multiple Acoustic Doppler Current Profiler (ADCP Workhorse, RD instruments with 307.7 kHz) moorings were installed in central Puyuhuapi channel in May, 2013 and from November 2013 to January, 2014. A scientific echosounder (SIMRAD 38 and 120 KHz) was used in the summer (January) and winter (August) 2014 to study plankton and fish distributions along the fjord. In order to validate the acoustic data, in-situ stratified zooplankton sampling was carried out with the aid of a Tucker trawl net. A strong diurnal vertical migration (DVM) of zooplankton was registered by the ADCP, with high/low backscatter signal during night/day. Zooplankton aggregated between the surface and ∼50 m depth at night, while during the day the aggregation was observed close to 100 m depth, indicating a downward migration during daylight hours. Along fjord acoustic 38 and 120 kHz echosounder sampling confirmed that zooplankton biomass concentrated during the daytime around 100 m depth in the Puyuhuapi fjord. Oxygen data obtained from a Conductivity, Temperature, Depth (CTD) profiler showed that from 100 m to ∼300 m depth the oxygen concentration decreased from 3 to 1 ml/l, confining the zooplankton to the first 100 m of the water column. Fishes were mainly observed close to zooplankton biomass and at some areas near the bottom during the day and night time. High concentrations of zooplankton were also observed around the sill in the Jacaf channel, evidencing that zooplankton tend to aggregate in regions of increased mixing. Combined acoustic methods (ADCP and scientific echosounders), thus, helped to understand zooplankton and fish distributions, zones of aggregation and DVM patterns in Patagonian fjords.