In the pelagic foodweb, micronekton at the mid-trophic level (MTL) are one of the lesser known components of the ocean ecosystem despite being a major driver of the spatial dynamics of their predators, of which many are exploited species (e.g. tunas). The Spatial Ecosystem and Population Dynamics Model (SEAPODYM) is a modelling framework that includes a representation of the spatial dynamics of several epi- and mesopelagic MTL functional groups. The dynamics of these groups are driven by physical (temperature and currents) and biogeochemical (primary production, euphotic depth) variables. A key issue to address is its parameterization for which we present a method using in situ acoustic data to estimate the parameters with a maximum likelihood estimation approach. The modeling of these components is central in the development of spatial population dynamics of larger predators, either protected species or exploited fish populations. A series of applications illustrate the recent advances in the continuous development of SEAPODYM, including the modeling of past history of tuna populations under the combined effect of climate variability and fishing exploitation, the projection of climate change and the progress in operational real time systems of monitoring.