The objective of this study was to estimate the surface flux of crustacean larvae at three points along the Baker/Martinez fjord complex, Chilean Patagonia, during the season of maximum river discharge. Concurrent acoustic Doppler current profiler (ADCP) and zooplankton surveys were conducted along three across-channel transects spanning 58 km along the fjord, in late February 2013. The results revealed a two-layer structure in along-channel residual velocity within the upper 25 m of the water column, which resembled a typical estuarine circulation pattern. Near the river mouth, transverse asymmetries in along-fjord flows and secondary circulation were found, which may substantially affect local patterns of larval transport and/or retention. Barnacle nauplii were more abundant during flood (15.2 ± 8.8 indiv m−3, mean ± standard error) than during ebb tide (3.36 ± 0.95 indiv m−3), suggesting they are tidally transported. Since the along-channel transport of vertically migrating larvae depends on the instantaneous flow fields to which they are exposed, larval abundance data were combined with velocity fields obtained from individual ADCP passes to produce instantaneous larval flux estimates. Near the Baker river mouth, net flux estimates showed that barnacle nauplii (cyprids) are advected landward (seaward), whereas zoeae of the squat lobster Munida gregaria are exported from the fjord. These results are consistent with previous findings and illustrate how the composition and distribution of meroplankton may reflect along-fjord changes in estuarine circulation, driven mostly by seasonal changes in freshwater inputs, as well as small-scale spatial variations in flow along the fjord.