The effects of a sudden rainfall (40 mm d-1) event on the surface waters covering muddy tidal flats were studied during April 2016 at the estuarine Cruces River wetland in south-central Chile (~40ºS). The study area included flooded vestigial tree trunks, which is evidence of coseismic subsidence associated with the 1960 Valdivia earthquake as a source of environmental variability. The tidal flat with vestigial tree trunks registered the fastest and highest depth of inundation. In contrast, the tidal currents velocity and total suspended solids' concentrations were higher at the flat without trunks. Sudden rainfall events can significantly modify the characteristics of surface waters above sedimentary intertidal surfaces, where structures such as flooded trunks are present.