Spatially distributed populations can exhibit source-sink dynamics. Despite long-standing interest in source-sink dynamics, identifying sources and sinks and quantifying their coupled dynamics in wild populations remains challenging. We used 26 years of data on reproduction, movement, and survival to estimate annual source-sink dynamics across the entire range of the endangered Everglade snail kite (Rostrhamus sociabilis plumbeus) during the invasion of a novel prey species. Populations underwent striking changes in source-sink dynamics over time since invasion. Our results illustrate how invasive species can cause impacts in uninvaded populations via changes in native species retention and emigration. Fluctuating emigration and retention alter long-term interpretations of source-sink dynamics through variation in local vs landscape contribution of populations to the metapopulation. Our study demonstrates that the status of ‘source’ or ‘sink’ can be highly variable through time and highlights how emigration is a key dimension of metapopulation dynamics, an insight with consequences for conservation.