Tropical streams have been intensively impacted by agricultural activities. Among the most important agricultural activities in Brazil, sugarcane production represents a large impact for economic development and for environmental conditions. Permeating sugarcane fields, several headwater streams can be affected by sugarcane cultivation, in special, aquatic biogeochemical cycles because of the deforestation, fertilization, crop residues and higher temperatures in the tropics. In this study, we analyzed the effects of sugarcane cultivation on methane fluxes and concentrations, assuming that carbon cycles are influenced by agricultural activities in headwater streams. Our study aimed to (1) measure methane fluxes and concentrations in tropical streams located in Southeastern Brazil, (2) Analyze whether seasonal cycles influence methane fluxes and concentrations, (3) Evaluate the influence of sugarcane cultivation on methane fluxes and (4) Analyze the association between water chemistry in the methane concentrations in tropical streams. We found mean fluxes of CH4 of 0.280 mmol m-2 d-1, with higher fluxes during the summer and in streams draining preserved catchments. The average CH4 concentrations were 0.695 µmol L-1, with higher values during the summer and in streams draining preserved catchments. Methane concentrations in the studied streams was influenced by dissolved oxygen (negatively), dissolved organic carbon (negatively), water velocity (positively) and conductivity (negatively). Methane concentrations were significantly higher than concentrations found in Temperate Grasslands, Savannas & Shrublands and similar to concentrations found in other tropical biomes (excluding Tropical & Subtropical Moist Broadleaf Forests which receives large amounts of organic inputs). We conclude that sugarcane influence methane concentrations and fluxes in tropical streams by reducing the organic matter availability provided by the native vegetation in soil and water.