Models of soil organic carbon (SOC) storage and turnover can be useful tools to analyse the effects of soil and crop management practices and climate change on soil organic carbon stocks. The aggregated structure of soil is known to protect SOC from decomposition and, thus, influence the potential for long-term sequestration. In turn, the turnover and storage of SOC affects soil aggregation, physical and hydraulic properties and the productive capacity of soil. These two-way interactions have not yet been explicitly considered in modelling approaches. In this study, we present and describe a new model of the dynamic feedbacks between soil organic matter (SOM) storage and soil physical properties (porosity, pore size distribution, bulk density and layer thickness). A sensitivity analysis was first performed to understand the behaviour of the model. The identifiability of model parameters was then investigated by calibrating the model against a synthetic data set. This analysis revealed that it would not be possible to unequivocally estimate all of the model parameters from the kind of data usually available in field trials. Based on this information, the model was tested against measurements of bulk density, SOC concentration and limited data on soil water retention and soil surface elevation made during 63 years in a field trial located near Uppsala (Sweden) in three treatments with different organic matter (OM) inputs (bare fallow, animal and green manure). The model was able to accurately reproduce the changes in SOC, soil bulk density and surface elevation observed in the field as well as soil water retention curves measured at the end of the experimental period in 2019 in two of the treatments. Treatment-specific variations in SOC dynamics caused by differences in OM input quality could be simulated very well by modifying the value for the OM retention coefficient epsilon (0.37 for animal manure and 0.14 for green manure). The model approach presented here may prove useful for management purposes, for example, in an analysis of carbon sequestration or soil degradation under land use and climate change.