Nutrient cycling in the sea is an organism-mediated process occurring at a vast range of temporal and spatial scales. Because of the traditionally physico-chemical orientation of marine ecosystem research, the relevant biological scales have not received adequate attention which, we claim, is the cause for the current stagnation and fragmentation in the state of the art. We argue that our knowledge of the natural history of pelagic systems is at a rudimentary level and that there is an urgent need for further development of this viewpoint in order to stimulate the course of future research and to provide an alternative framework for interpretation of existing data sets. We compare terrestrial with pelagic systems and indicate the fundamental difference in the relationship between auto- and heterotrophs of the two system types. Because functioning pelagic systems are not easily accessible to direct visual observation, it is necessary to formulate speculative hypotheses about possible organism strategies in relation to specific features of the physico-chemical environment than can then be tested under laboratory and field conditions. A tentative scheme for classification of pelagic systems based on temporal and spatial patterns of nutrient cycling is developed. Within this framework, we draw attention to the crucial role played by mucus as a carrier and binding agent in pelagic systems but also as an energy source in regenerating systems. We further suggest that the common herbivorous copepods condition their environment by their feeding behaviour and contribute to maintenance of a microbial community which is of survival value to them. Finally, we give two examples of organism control of physicochemical properties of the environment. The purpose of this article is to encourage conscious development of an ecological paradigm as a base for marine ecosystem research. © Taylor and Francis Group, LLC.