A one-dimensional coupled physical and intermediate-complexity biochemical model comprising large and small phytoplankton and zooplankton groups, particulate organic nitrogen, ammonium and nitrate was developed to study the physical-biogeochemical interactions and parameters that control plankton production in the Alboran and Balearic Sea ecosystems. The model findings suggest that pelagic fish predation and resource availability through lateral and vertical nutrient inputs jointly characterize the plankton community structures. In agreement with previous observations, a typical annual plankton structure of the mesotrophic systems involves a vertically homogeneous biomass of large groups of phytoplankton and zooplankton within the upper 50-to-100 m layer from mid-November to April and a subsurface biomass accumulation distributed roughly within 25-75 m depths in the following months. Their light and temperature limitations constrain the smaller groups into the thermocline zone (25-50 m) during late spring and summer. These obtained results were dependent on the zooplankton actively switching between preys (i.e., the food preference coefficients dependent on prey biomass). In the case of no switching, spurious dynamic equilibrium solutions may arise in the case of a constant and weak fish predation rate and using the quadratic predation formulation. The choice of a Holling Type II (i.e., hyperbolic) predation function may, however avoid ambiguous representation of the annual plankton structure in the case of a constant food preference choice under relatively weak predation pressures. (C) 2013 Elsevier Ltd. All rights reserved.