Small pelagic fish species are keystone species in upwelling ecosystems due to their dominant biomass and role in transferring energy from low trophic levels to top predators. These ecosystems are often termed “wasp-waist” because few small pelagic species dominate and manage this energy transfer. Atmospheric variability leads to fluctuations in upwelling intensity, duration, and extent, creating complex responses from small pelagic fish species. This complexity involves factors like fish migration, larval retention, predation, competition, fishing, food, oxygen, and temperature limitations. Increasing studies demonstrate that spatially explicit biophysical individual-based models, driven by precise hydrodynamic and biogeochemical simulations, can capture much of this complexity. Sensitivity tests on such models provide significant insights into the main drivers of small pelagic fish biomass variability. We present a generic, adaptable model for various small pelagic fish species and regions, capable of full life cycle multi-generational studies. The model explores age truncation effects, homing behavior, and evolutionary impacts. Using Sardinella aurita off North-West Africa as a case study, we simulated the hydrodynamic and biogeochemical environment with coupled regional models (ROMS-PISCES) over 05°-40°N and 05°-30°W at ~8 km resolution from 1980-2009. This approach suits data-poor ecosystems, requiring (1) validated inter-annual hydrodynamic and biogeochemical simulations, (2) specific Dynamic Energy Budget parameters, and (3) basic rules for fish school kinematics. This framework helps analyze fish spatio-temporal distribution and biomass complexities, achieved by comparing modeled and observed fish populations through Pattern Oriented Modelling.