Resource partitioning is the basis of the coexistence of sympatric species and has therefore received much attention in ecological studies. However, how variation in environmental conditions (and particularly natural variation in resource availability) can influence resource partitioning in free-ranging animals is not well understood. In the present study, we addressed the hypothesis that natural changes in the availability of food resources affect food partitioning between sympatric species. To do so, we examined temporal changes in the plasma isotopic signature (δ15N and δ13C) of syntopic Lincoln’s sparrows Melospiza lincolnii and white-crowned sparrows Zonotrichia leucophrys, in parallel with seasonal changes in habitat maturity and food availability from spring to early summer. We found no apparent trophic segregation between Lincoln’s and white-crowned sparrows when resources were scarce in spring. But, interestingly, as resource availability and the number of breeding birds increased, Lincoln’s sparrows showed lower δ15N values than white-crowned sparrows, as they consumed more prey from lower trophic levels and less prey from higher trophic levels. This feeding divergence between sympatric species may be explained (1) by a change in foraging preferences and opportunities for Lincoln’s sparrows and (2) by the abundance of competitors that increased faster than resources, thus promoting interspecific competition and trophic segregation. These results provide clear evidence that trophic segregation is dynamically tied to variation in environmental conditions, which are therefore fundamental to consider when examining resource partitioning between co-existing species.