The effects of climate change on lake surface water temperature (LSWT) have been well documented in the northern hemisphere but are less understood in the south, particularly in shallow lakes. Here we investigated the warming rates of three large shallow lakes in southern Brazil using a comprehensive 60 year meteorological data set and a 20 year LSWT time series derived from MODIS. Our findings reveal substantial and consistent regional lake water warming concentrated in spring (0.5 °C dec −1 ) and, to a lesser extent, summer (mean trend of 0.3 °C dec −1 ) and annual trends (0.3 °C dec −1 ), in fair agreement with air temperature trends. The data showed an increase in mean, maximum, and minimum air temperatures in these periods, along with a shortening of the cold season for air (−6.3 days dec −1 ) and water (−11.6 days dec −1 ), with all these changes exhibiting heightened intensity in the last 20 years. The remote sensing data showed a fair homogeneity in the warming rates within the lakes but marked spatial differences, possibly owing to the effects of climate change on the tributaries. The warming rates found here can result, for example, in anticipation of phytoplankton phenology and alteration in the functional groups, while the spatial differences in the warming may have additional ecological impacts.