A total of 600 serum samples from five farms were collected and the geographic coordinates of each farm were georeferenced to establish two Köppen climate classes (wet tropical and tropical rainforest). Serum samples were examined by commercially available enzyme-linked immunosorbent assay (ELISA) kits to detect antibodies against N. caninum and T. gondii, while anti-B. abortus antibodies were analysed using the Rose Bengal test and ELISA kit. The overall estimated prevalence of N. caninum, T. gondii and B. abortus was 41.2%, 30.7% and 0.5%, respectively. The highest percentages of positive buffaloes with neosporosis and toxoplasmosis were found in the states of Tabasco (46.7%, wet tropical climate) and Veracruz (32.7%, tropical rainforest climate), respectively. Multivariate logistic regression showed that N. caninum seropositivity in buffalos was associated with the normalized difference vegetation index (NDVI) (OR: 1.068; 95% CI: 1.026-1.112; P = 0.001) and tropical climate regions (OR: 1.737; 95% CI: 1.112-2.712; P = 0.015). In addition, statistical analysis revealed that sex (OR: 1.737, 95% CI: 1.685-9.737; P = 0.002), NDVI (OR: 1.382; 95% CI: 1.095-1.746; P = 0.007) and rainfall (OR: 1.478; 95% CI: 1.110-1.967; P = 0.007) were significant risk factors for T. gondii infections. These results indicate that the potential impact of the risk factors was different for each disease in buffaloes, which may be useful for developing regionally adapted control strategies and preventive measures.