Abstract Resource subsidies of energy and nutrients can be transported via physical forces, such as gravity, wind or water and biotic processes, such as animal migration or emigration. Migratory transport of nutrient subsidies may be associated with reproductive processes, such as the deposition of eggs or emigration of juveniles to adult habitats. We quantified net nutrient fluxes associated with amphibian migrations across aquatic–terrestrial boundaries of eight temporary ponds in Illinois, USA. We measured carbon (C), nitrogen (N) and phosphorus (P) subsidies from terrestrial environments to ponds, in the form of eggs, and the reciprocal subsidies from ponds to terrestrial environments via juvenile emigration. Juvenile emergence biomass did not follow patterns of egg biomass, as not all species bred successfully in each pond, resulting in variability in the magnitude of nutrient fluxes both across ponds and species. The terrestrial environment was not always the recipient system of net nutrient fluxes. Hydroperiod, trophic interactions and species composition explained some dynamics of N and P subsidies. Anthropogenic alterations that affect amphibian communities, such as habitat fragmentation and conversion for agriculture and urbanisation, could have large‐scale impacts on nutrient fluxes and connectivity of temporary pond–forest systems.