Modeling has emerged as a critical tool to investigate a wide range of biogeochemical and ecological challenges in the sea, such as the impact of climate change on the air–sea balance of carbon dioxide. Models need to be formulated and adapted to address a particular problem, and are therefore seldom easily transferable. The core set of processes to be captured by ocean biogeochemical/ecological models is the ‘great biogeochemical loop’, which starts with the photosynthetic fixation of inorganic elements into organic matter by phytoplankton, and then follows the transport of these elements into the ocean’s interior in organic form and then back to the surface in their inorganic forms. As the latter occurs by mixing and transport, ecological/biogeochemical models in the ocean invariably need to be coupled to some form of physical model. The complexity of either the physical or the biogeochemical/ecological models can vary greatly, leading to a large diversity of coupled physical ecological/biogeochemical models, ranging from simple box models to complex three-dimensional models that incorporate many bioreactive elements and functional groups. Emerging modeling directions are the increased interaction of observations and models through inverse methods and the continuing expansion of systems that these models are coupled to, such as the sediments, atmosphere, and the land.