As ecosystems change, understanding the consequences for fish population dynamics and habitat use is essential for their management. Using white perch (Morone americana) survey data on early life stages collected during a long-term ichthyoplankton monitoring program in the Hudson River (New York, USA), an ecosystem under immense pressure from climate change, ecological shifts, and anthropogenic activities, we evaluated the drivers of changes in egg abundance and spawning habitat between 1980-2017. Results indicated that egg abundance is associated nonlinearly with temperature, conductivity, discharge, depth, location, and the week of year. Additionally, large changes in hotspots of spawning activity within the Hudson River were identified and the lower extent of spawning habitat has moved upriver since 1980. We also found that egg abundance has declined within the river over time. This study indicates that the dynamics of white perch early life histories and spawning habitat are changing. It also highlights the utility of a long-term monitoring program for broadening our understanding of fish ecology in the age of big data in changing ecosystems.