The spatial and temporal variability of water levels was investigated across a section of floodplain in the Pantanal that represents typical geomorphic and ecological complexity of these environments. A series of 11 staff gauges were installed along a 12-km transect running perpendicularly from the Cuiabá River into the floodplain. The staff gauges were monitored fortnightly during the flood seasons from 2004 to 2007. Contrary to what is often assumed, the water surface profile was never level, and it was particularly variable when there was less water on the floodplain. Water surface slope varied from 1.4 × 10⁻⁴ (unitless) to 1.3 × 10⁻³ indicating substantial water movement that was verified by flow observations. The spatial patterns of water level variation were repeated across years, even though there was considerable interannual variation in magnitude and duration of floodplain inundation. In 2004 and 2005, the duration of inundation was 121 and 120 days, respectively, but in 2006 and 2007, inundation lasted 166 and 157 days, respectively. These observations reveal considerable small-scale spatial variability in the water surface profile, but with persistent patterns over space and time that are related to the river hydrograph and the channels that convey flood waters across the area. This study contributes to our understanding of inundation hydrology and its linkages to ecosystem processes, and additionally provides a valuable data set for calibration and validation of remote sensing approaches to measurement of inundation area and water movement across floodplains.