Widespread extirpations of amphibian populations are well-documented, yet ecosystem-level effects of these losses are poorly understood. Larval amphibians have the potential to significantly alter algal communities and seston, particularly in tropics where amphibian abundance and diversity are high. As part of the Tropical Amphibian Declines in Streams (TADS) Project, we examined long-term (> 4 years) changes of algal periphyton quality and quantity in an upland Panamanian stream, both with and without tadpoles, in response to a catastrophic die-off of stream-breeding frogs. Monthly sampling of natural stream substrate showed increased levels of chlorophyll a (+180%), ash-free dry mass (+210%), and inorganic sediments (+160%) during the post-extirpation period relative to pre-extirpation. Periphyton δ¹⁵N decreased during post-extirpation, suggesting an alternate source of N for uptake by algae. The quality of seston, as measured by C/N, decreased after tadpoles were extirpated from the stream. Our data indicate that stream-dwelling larvae alter periphyton quality and quantity and seston quality, and the effects of tadpole losses on streams may persist long term.