Persistent funding shortfalls undermine protected areas (PAs) worldwide, yet few studies analyse these patterns across space and time. We examined funding deficits in 300 Brazilian federal PAs from 2014 to 2023 using spatial Durbin error models. Deficits were measured as the gap between evidence-based minimum management costs and actual spending. We analysed how PA age, size, management group, ecological region, population density and per capita GDP predict deficits, decomposing socioeconomic effects into direct and spillover components. In 2023, 72% of the PAs faced deficits totalling 958 million international dollars, despite a 30% investment increase over the decade. Larger PAs had greater shortfalls; older PAs had smaller ones. Amazon PAs averaged 79.2% deficits versus 27.6% in the Atlantic Forest. No significant difference emerged between management types. Higher population density predicted lower deficits, probably reflecting greater political visibility near urban centres. No direct local GDP effect was detected, but spillovers from neighbouring high-income regions suggest regional prosperity influences PA funding through spatial networks. Funding deteriorated in 2020–2021 amid fiscal contractions and policy shifts, then recovered in 2022–2023. These findings reveal deep structural inequities, particularly in the Amazon, highlighting the need for transparent national PA financing systems.