SummaryBackgroundEnvironmental degradation facilitates the emergence of vector-borne diseases, such as malaria, through changes in the ecological landscape that increase human–vector contacts and that expand vector habitats. However, the modifying effects of environmental degradation on climate–disease relationships have not been well explored. Here, we investigate the rapid re-emergence of malaria in a transmission hotspot in southern Venezuela and explore the synergistic effects of environmental degradation, specifically gold-mining activity, and climate variation.MethodsIn this spatiotemporal modelling study of the 46 parishes of the state of Bolívar, southeast Venezuela, we used data from the Venezuelan Ministry of Health including population data and monthly cases ofPlasmodium falciparummalaria andPlasmodium vivaxmalaria between 1996 and 2016. We estimated mean precipitation and temperature using the ERA5-Land dataset and used monthly anomalies in sea-surface temperature as an indicator of El Niño events between 1996 and 2016. The location of suspected mining sites in Bolívar in 2009, 2017, and 2018 were sourced from the Amazon Geo-Referenced Socio-Environmental Information Network. We estimated measures of cumulative forest loss and urban development by km2using annual land cover maps from the European Space Agency Climate Change Initiative between 1996 and 2016. We modelled monthly cases ofP falciparumandP vivaxmalaria using a Bayesian hierarchical mixed model framework. We quantified the variation explained by mining activity before exploring the modifying effects of environmental degradation on climate–malaria relationships.FindingsWe observed a 27% reduction in the additional unexplained spatial variation in incidence ofP falciparummalaria and a 23% reduction inP vivaxmalaria when mining was included in our models. The effect of temperature on malaria was greater in high mining areas than low mining areas, and theP falciparummalaria effect size at temperatures of 26·5°C (2·4 cases per 1000 people [95% CI 1·78–3·06]) was twice as high as the effect in low mining areas (1 case per 1000 people [0·68–1·49]).InterpretationWe show that mining activity in southern Venezuela is associated with hotspots of malaria transmission. Increased temperatures exacerbated malaria transmission in mining areas, highlighting the need to consider how environmental degradation modulates climate effect on disease risk, which is especially important in areas subjected to rapidly rising temperatures and land-use change globally. Our findings have implications for the progress towards malaria elimination in the Latin American region. Our findings are also important for effectively targeting timely treatment programmes and vector-control activities in mining areas with high rates of malaria transmission.FundingBiotechnology and Biological Sciences Research Council, Royal Society, US National Institutes of Health, and Global Challenges Research Fund.