In the prolific literature on the impact of environment on migration, direct and indirect effects are often mentioned but rarely estimated separately. We use structural equation modelling to estimate how the drivers of migration (socio-economic, environmental and individual) interact with each other and jointly contribute to individuals’ migration decision in rural Burkina Faso (1970–1998). Facing a worsening environmental situation, people’s direct response tends to be short-term migrations to rural and urban areas, but the indirect effect differs: poor rainfall conditions push down socio-economic situation in communities, which in turn discourages migration to rural areas or to abroad. In total, an adverse environmental situation tends to increase the likelihood of short-term migrations to rural and urban areas and to decrease that of long-term migrations to rural areas and to abroad. These findings contribute to a clearer understanding of the migration response to poor environmental conditions.