Seasonal differences in marine size spectra of micronekton at the shelf-ocean interface of the northern (NBUS) and southern Benguela Upwelling System (SBUS) in Feb-Mar 2019 and Sep-Oct 2021 were analysed. It was distinguished between mesopelagic fishes and total micronekton, comprising both the invertebrate and the vertebrate components. The metabolic theory of ecology (MTE) model containing a resource and a temperature term and a term representing a transfer function was applied to test three different types of size spectra slope estimates. The model fitted best with linear slopes calculated of log-binned averaged community biomass (LBNbiom method), while maximum likelihood without binning and quantile regression estimates without averaging proved less effective. The best model for total micronekton contained significant effects both for resource term and transfer function, but not for temperature. Normalized biomass size spectra slopes of the total micronekton were in the range predicted by MTE ranging between -0.80 and -1.37, and NBUS slopes were steeper than SBUS slopes in both seasons. The slopes for the fishes’ subcomponents were less steep ranging from -0.23 to -0.92, where values > -0.75 fall outside the theoretical range, suggesting that selecting taxonomic subsets for size spectrum analysis is problematic. The importance of the productivity regime shaping the biomass spectrum directly through the resource level and indirectly through the transfer function is highlighted.