Amphibians are the most endangered vertebrate taxa, facing population declines worldwide. Amphibians, as well as their microbiome, are highly susceptible to pollution associated with agriculture and urbanization land use conversion. Glyphosate, the most widely used herbicide in the US, is an immunosuppressant, increasing species vulnerability to infectious diseases and pathogens. A direct relationship between the gut microbiome, digestive, immune, metabolic, and neurobehavioral processes exists. Disturbances of the gut microbiome leads to health disruption. We explored the effects of glyphosate and antibiotics in the growth and behavior of Rana berlandieri tadpoles. We quantified the gut microbiome bacterial diversity of tadpoles reared in one of four treatments: (1) an environmentally relevant, but non-lethal, concentration of glyphosate, (2) an antibiotic cocktail to excise tadpoles of their natural microbiome, (3) both glyphosate and antibiotics (combination), and (4) a control group. We also measured growth every 3 days. After 11 days we quantified activity and after 14 days we collected the gut from 2 tadpoles per tank. The remaining tadpoles were moved to untreated water and reared for 2 months to measure recovery. Tadpoles in the combination and antibiotic treatments had lower growth compared to control tadpoles. Control tadpoles were more active than tadpoles in other treatments. After recovery, glyphosate exposed tadpoles grew larger than control tadpoles. Behavior results indicate that tadpoles exposed to glyphosate become lethargic. A disturbed microbiome results in lower growth rates, lethargy, and delayed development. Glyphosate use should be avoided to maintain a healthy microbiome, especially when tadpoles are developing.