This study aimed to examine the spatial organization of pelagic communities within the water column along a horizontal gradient extending from the coast to the offshore area, categorized into three zones: inshore, offshore, and transition. A total of 29,000 nautical miles of acoustic transects collected during 14 annual standardized surveys were analyzed using two complementary acoustic methods: (i) extraction of sound scattering layers (SSL) and (ii) echointegration (EI) across the entire water column, both horizontally and vertically averaged.  The results revealed significant differences between the three bathymetric areas based on SSL and EI descriptors, with nektonic communities in the transition area exhibiting intermediate characteristics between those in the inshore and offshore areas. The relative abundance of nektonic communities decreased from shallow coastal areas to deep offshore areas. The inshore area is different from transition and offshore area, which is confirmed by diel vertical migration (DVM) analyse through vertical profiles. All areas exhibited classic DVM type I; however, offshore and transition areas also presented unexpected DVMs of type II, i.e., organisms descend deeper during the night, displaying distinct vertical profiles compared to the inshore area. This suggests that the functional and specific composition of pelagic nektonic communities differed between inshore and offshore areas, indicating that organisms adjust their responses to their environment. Over two decades, the three bathymetric areas showed a significant increase in pelagic relative biomass and variation in SSL spatial structure. Nevertheless, nektonic communities reacted differently to interannual changes depending on the bathymetric areas, such as the minimal depth of the shallowest SSL. Fluctuations in SSL descriptors were highlighted over the study period, which may be related to multi-decadal oscillations in the Atlantic Ocean.