Sea-level rise is causing an increase in tidal flooding in coastal urban areas. Extreme high tides, also known as king tides, are peak tide moments in which tidal amplitude is increased and shallow groundwater flows from the underlying water table are introduced. During tidal flooding in urban areas, accumulated anthropogenic indicators of different water sources are released from groundwater to surface waters, but how these tidal events affect the contributions of different water sources to urban flood waters is uncertain. We quantified tracers of anthropogenic origin including fluoride, fecal coliform bacteria, as well as dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) composition from inflowing and outflowing waters of Wagner Creek and the Coral Gables waterway (Miami, Florida, USA) during a king tide event. We measured higher DOC and fluoride concentrations at downstream coastal sites of both transects that decreased upstream, and during tidal flooding concentrations of both were highest in fall tide waters compared to rising and peak tides. Tidal flooding increased anthropogenic indicators (fecal coliform and fluoride) in urban surface waters, and we measured higher levels of both in Coral Gables waterway than in Wagner Creek. Biological Index values associated with DOM were higher upstream in Wagner Creek and downstream in Coral Gables waterway. Tidal influence and proximity to the coast were important determinants in our ability to detect municipal and wastewater indicators. Extreme high tide events pose threats to low-lying communities as increasing sea level rise will lead to prominent concentrations of anthropogenic signatures causing environmental stress and imminent threats to public health as groundwater inundation continues to pollute surface waters.