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Southern flounder (Paralichthys lethostigma) are a coastal flatfish species that supports recreational and commercial fisheries but are currently experiencing range‐wide declines. To quantify the range‐wide declines and investigate the role of climate in these declines, fishery‐independent sampling data of age‐0 flounder were obtained from 34 estuaries representing four states in the Gulf of Mexico (TX, LA, AL, and FL) and three states in the Southeastern United States Atlantic Ocean (FL, SC, and NC) spanning from 1976 to 2019. Generalized additive models (GAM) were used to estimate age‐0 recruitment trends. Spatial and temporal synchrony analyses were then conducted using annual GAM‐predicted values to determine if trends were similar between estuaries in close proximity, and if declines occurred at the same time. Because the species is dependent on physical transport (i.e., winds and tides) for recruitment, hourly wind speed, wind direction, water temperature, and air temperature were obtained for estuaries with non‐zero sampling totals and long‐term data sets. Only six estuaries showed significant relationships between age‐0 flounder indices and growing degree days. However, all estuaries with wind data showed significant relationships between age‐0 flounder indices and hourly summed wind speed. Southern flounder also have environmental sex determination, meaning warming estuaries could also account for population changes and declines. We document that water temperatures in the same space and time where southern flounder sexually determine are warmer now than even a decade ago, which could masculinize populations and substantially change population demographics. These results illustrate the vulnerability of estuarine finfish populations to climate change and increased climate variability. Understanding how climate acts on southern flounder biology may help managers respond to and prevent fishery collapses.