Land use change drives significant declines in ecosystem services globally. However, we currently lack an understanding of how and where different beneficiaries of ecosystem services experience the impacts of land use change. This information is needed to identify possible inequalities in the delivery among beneficiaries, and to design policy interventions to address them. Here, we used a spatially explicit and disaggregated approach to ask how land use change affects the distribution of flood protection among three beneficiary sectors (urban residents, rural communities, and the food sector). Our study focused on the Brigalow Belt Bioregion of Australia – an area affected by widespread deforestation – and assessed the effect of land use change on flood protection between 2002 and 2015. We estimated flood protection per beneficiary sector as the total upstream runoff retention (supply) linked to areas where flood protection is required for sector-specific infrastructure (demand). We calculated changes in flood protection between 2002 and 2015 at the local government area scale and for each beneficiary sector. Using counterfactual scenarios, we identified whether changes in flood protection were driven by forest loss or changes in the extent of infrastructure at risk of flooding. We found net declines in flood protection for all sectors. Urban residents experienced the greatest decline (28%), followed by rural communities (15%), and the food sector (14%). Overall declines in flood protection across the whole region were driven primarily by forest loss. However, for some local government areas and beneficiaries, changes in flood protection were also driven by increases in forest cover or spatial changes in demand. Recognition that beneficiary sectors can be impacted via different drivers of change is fundamental to revealing highly impacted sectors. In turn, this information can be used to develop management strategies to address inequalities in the distribution of ecosystem services among beneficiaries.