We examined the effects of landscape changes in an environmental gradient of forest, a Vernicia fordii plantation, and crops on the distribution patterns of amphibians in San Rafael National Park. We conducted eight periods of fieldwork between June 2012–April 2013 and used pit fall traps with drift fences to capture amphibians. We recorded eight species of the families Bufonidae, Leptodactylidae, and Odontophrynidae. The environmental variables correlated with the abundance of amphibians were relative humidity, litter depth, herbaceous cover, and air temperature, and significant differences were found in species composition. Generalist species like Leptodactylus mystacinus and Physalaemus cuvieri were found in the most altered areas such as crops and the plantation. Rhinella ornata and Proceratophrys avelinoi were primarily restricted to primary forests, and their abundance was sensitive to forest lost and degradation. Our results support the idea that modified habitats influence distribution patterns of amphibians, and the protection of the remnants of pristine Atlantic Forest is a critical step in the conservation of anuran biodiversity in Paraguay.