In the Coleambally irrigation area (NSW, Australia), the occurrence of four tadpole and frog species in rice bays on farms growing either rice only or both rice and corn was studied over two seasons. In addition to analysis of species occurrence, both gonadal histology and assessment of Batrachochytrium dendrobatidis infection rates were performed. The rice acreage available as potential tadpole habitat was extensively distributed throughout the irrigation area, but more corn was grown in the northern region compared with the southern region. The mean abundance of Litoria raniformis tadpoles was significantly lower in the northern sites compared with the southern sites. In contrast, tadpoles of Limnodynastes fletcheri, Limnodynastes tasmaniensis, and Crinia parinsignifera had a uniform distribution across all study sites. A principal components analysis showed a relationship between farm type and the rice herbicide applied when the crops were initially sown, with sites occupied by Litoria raniformis in the beginning being predominantly rice-only farms. A discriminant analysis showed that low concentrations of the corn herbicide metolachlor and increased pH were the main variables studied that determined site occupation by L. raniformis. This suggested that farms growing only rice (and not corn) with high algal production were the preferred sites. The rates of chytrid infection and gonadal malformations were low across both regions. Histology of the gonads of metamorphs showed that L. raniformis gonadal differentiation is slow compared to that of the two Limnodynastes species. We concluded that farm practices associated with increased corn cropping in the northern region, rather than any direct effect of corn herbicides, determine the reduced presence of Litoria raniformis in the northern region.