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The reduction of the computational effort is desirable for the simulation of marine ecosystem models. Using a marine ecosystem model, the assessment and the validation of annual periodic solutions (i.e., steady annual cycles) against observational data are crucial to identify biogeochemical processes, which, for example, influence the global carbon cycle. For marine ecosystem models, the transport matrix method (TMM) already lowers the runtime of the simulation significantly and enables the application of larger time steps straightforwardly. However, the selection of an appropriate time step is a challenging compromise between accuracy and shortening the runtime. Using an automatic time step adjustment during the computation of a steady annual cycle with the TMM, we present in this paper different algorithms applying either an adaptive step size control or decreasing time steps in order to use the time step always as large as possible without any manual selection. For these methods and a variety of marine ecosystem models of different complexity, the accuracy of the computed steady annual cycle achieved the same accuracy as solutions obtained with a fixed time step. Depending on the complexity of the marine ecosystem model, the application of the methods shortened the runtime significantly. Due to the certain overhead of the adaptive method, the computational effort may be higher in special cases using the adaptive step size control. The presented methods represent computational efficient methods for the simulation of marine ecosystem models using the TMM but without any manual selection of the time step.