Destructive coastal floods are commonly increasing in frequency and may be caused by global precipitation intensification. Such connections through climate, watershed, and river processes are poorly understood because of complex interactions in transitional fluvial-marine environments where flooding is caused by rivers, marine storm surge, or both in compound events. To better understand river floods along the fluvial-marine transition, we study watersheds of the northeastern Gulf of Mexico using long-term observations. Results show intensifying precipitation decreased precipitation-discharge lag times, increasing river-flood frequency and the likelihood of compound events in fluvial-marine transitions. This reduction in lag time occurred when the Atlantic Multidecadal Oscillation and El Niño Southern Oscillation began strongly affecting river discharge through the advection of moist air, intensifying precipitation. Along the fluvial-marine transition, compound events were largest in inland reaches. However, for inland reaches, compound event water levels did not exceed the floods caused solely by river flooding, the largest flood hazard in these systems. Our results demonstrate precipitation and river discharge play critical roles in coastal flooding and will likely escalate flooding as the climate continues to warm and intensify precipitation.