Understanding the relationship between sound-scattering layers (SSLs) and pelagic habitat characteristics is a substantial step to apprehend ecosystem dynamics SSLs are detected on echo sounders representing aggregated marine pelagic organisms. In this study, SSL characteristics of zooplankton and micronekton were identified during an upwelling event in two contrasting areas of the Senegalese continental shelf. Here a cold upwelling-influenced inshore area was sharply separated by a strong thermal boundary from a deeper, warmer, stratified offshore area. Mean SSL thickness and SSL vertical depth increased with the shelf depth. The thickest and deepest SSLs were observed in the offshore part of the shelf. Hence, zooplankton and micronekton seem to occur more frequently in stratified water conditions rather than in fresh upwelled water. Diel vertical and horizontal migrations of SSLs were observed in the study area. Diel period and physicochemical water characteristics influenced SSL depth and SSL thickness. Although chlorophyll-a concentration insignificantly affected SSL characteristics, the peak of chlorophyll a was always located above or in the middle of the SSLs, regularly matching with the peak of SSL biomass. Such observations indicate trophic relationships, suggesting SSLs to be mainly composed of phytoplanktivorous zooplankton and micronekton. Despite local hypoxia, below 30 m depth, distribution patterns of SSLs indicate no vertical migration boundary. The results increase the understanding of the spatial organization of mid-trophic species and migration patterns of zooplankton and micronekton, and they will also improve dispersal models for organisms in upwelling regions.