Spatially and temporally continuous temperature measurements were collected over 32 h using a fiber-optic distributed temperature sensing (DTS) system deployed along 330 m of two intertidal saltmarsh channel beds in northern California. Measured temperature gradients imparted ecosystem-scale structure to the saltmarsh tidal channel thermal regime, which was punctuated by potential warm and cold refugia. Anomalous bed temperatures of 2-4 degrees C occurred throughout the 1.3 tidal cycles at some locations. Discrete locations of consistently warm temperatures characterized sustained seepage of recently infiltrated tidal waters. Low-variance temperature anomalies were typically collocated with hidden microtopographic tributaries that facilitated mixing of warm surface waters and cold groundwater. Bed temperature gradients (approximately 2 degrees C/100 m, average) decreased from high temperatures similar to bay water at the channel mouths to low inland temperatures comparable to groundwater. The trends were maintained by cold groundwater discharge throughout the channels, which affected bed temperatures in proportion to channel reach exposure time; the opposing effect, conductive bed-warming by tidal waters, was proportional to flood duration. DTS is a promising tool for identifying spatial and temporal temperature patterns of hydroecological importance amidst complex natural systems.