The conversion of natural habitats to agriculture results in the structural, physical and chemical degradation of ecosystems; and microbial communities respond to change with shifts in diversity and environmental function. Because the structure of amphibian-associated microbiome depends partially on the dynamics of microorganisms in the habitat, we hypothesized that land use would affect the tadpole skin microbiota structure of populations inhabiting water bodies in agricultural lands. To study this, we sampled microbial communities of water bodies and skin of larval amphibian across a gradient of land use intensification represented by cerrado, pastures and soybean fields. We used 16S rRNA high-throughput gene sequencing to characterize the microbial communities. Land use had a strong effect on both host and habitat bacterial communities. Bacterial ASVs richness and diversity in water bodies decreased from pristine habitat to soybean plantations, with the cerrado community differing from pasture and soybean fields. The aquatic microbial community composition and structure were different across the gradient, showing a robust effect of land use on this habitat. The richness and diversity of amphibian-associated bacterial community was lowest in cerrado and highest in pasture populations. The soybean plantation exhibited the most distinct composition and structure of amphibian microbiota while the pasture and cerrado communities were similar. Bacterial ASVs, candidates for biomarkers of the land use effect on both host and water bodies communities, were indicated. Our results highlight the effects of land use intensification as a driver for amphibian microbiome and offer information on the functionality of agro-industrial environments.