The Benguela Current Large Marine Ecosystem (BCLME) is situated along the coast of south-western Africa, stretching from Tombua (Angola) in the north (16°N, 11°W) southwards to the east of the Cape of Good Hope (South Africa) (29°S, 17°E) and includes the study zone, from 17°S, 9°E to 31°S, 17°E. In this work, we focused on the Namibian continental shelf where fishing activities are mostly due to industrial fishing. Acoustic data were recorded with a 38 kHz echosounder, from 10 to 500 m depth over 8 surveys totalling 46 302 nmi from 1994 to 2001. To get homogenous data (i) only off-upwelling season surveys (October to June) were studied and (ii) only continental shelf data were considered (10-150 m). The mean volume backscattering strength (Sv in dB) was used as a micronektonic biomass proxy to assess its spatial inter-annual variability. Diel transition periods were removed from analyses to avoid micronektonic density changes bias due to diel vertical migrations. Data were echointegrated at a spatial resolution of 0,1 nmi*1 m depth using the Matecho tool. (i) On horizontal dimension, the variability in annual micronektonic densities was assessed using the mean Sv value for each 0,1 nmi Elementary Sample Unit (ESU). Then, hot and cold spots were computed from the combined analysis of the spatial correlation and the Moran's I index of these values. (ii) On vertical dimension, the change of micronektonic spatial structure between day and night was assessed using the mean Sv value for each 1 m depth step. The inter-annual variability inside the eastern boundary upwelling ecosystem of the BCLME was analysed. (i) No significant change in micronektonic density was observed over the study period. Mean micronektonic acoustic density values observed were lower than in other African Atlantic large marine ecosystems. (ii) Hot and cold spots were spatially stable over time. Further analysis of physico-chemical parameters should improve the understanding of this pattern. (iii) A different vertical structure was reported between day and night, suggesting a migration from bottom to surface at dusk, as in the well-known diel vertical migrations. In perspective, physical processes occurring in the water column from turbulence to mesoscale activities should be considered in future studies.