Our modelling approach allows for creating transparent models of complex dynamic systems (e.g. man-made urban systems, biological systems, agro-ecological systems, socio-economic systems, etc.) characterized by accumulations (delays) and non-linear feedback mechanisms (e.g. causal effects of atmospheric composition on biodiversity and vice versa) that explicitly reflect the relationship between cause and effect. Our models help to understand how the main elements of some specific system interact with each other over time to determine the structural origin of some identified problem behaviour and to design and assess favourable policies that may effectively govern the system in the future (e.g. changes in share of specific species, novel business models, taxation strategy, etc.). With our approach, it is possible to forecast e.g. changes in an environmental system and their drivers, ecosystem response to climate change, impact of biodiversity change on climate, effects of agrobiodiversity on sustainability, socio-economic changes, etc. Finally, our models help to identify what policies and modifications in the structure have to be implemented to cause a more favourable behaviour in the system.