Despite significant milestones in armed conflict research generally and climate security research specifically, methodologically tight explanation of naturally caused armed conflict still leaves much to be desired. In this article we unpack the black box of the climate-security nexus and advance causal modelling of armed conflict. To infer effects of natural causes on armed conflict outcomes, we apply recent advances in causal methods to conflict outcomes that have been non-experimentally observed across Iraqi municipalities. Retrieval of an entire empirical causal structure of climate-conflict pathways allows us to corroborate the existence of a cause-and-effect relationship between climatological, environmental, and demographic variables and armed conflict. We confirm that soil temperature, population density, and variability of latent energy cause an increase in fatalities, while rice production decreases fatalities. We discuss our findings, their limitations, and future research directions, and reflect on their relevance for policy interventions.