The effects of free-floating mats of the water hyacinth Eichhornia crassipes (Mart.) Solms on the limnological characteristics of two lakes located on the fringing floodplain of the lower Paraná River (27°27'S, 58°55'W) were studied monthly between April 1998 and April 1999. The mobility of the free-floating vegetation at both locations prevented continual observation. Therefore, to carry out the intensive sampling needed for this study, two experimental ponds (A and B) were filled with water from the Paraná River in 1996. Pond A was designed to reproduce conditions similar to those of lakes vegetated with water hyacinth. Pond B was designed to recreate the limnological conditions of these lakes, such as a high concentration of dissolved and fine particulate organic matter and a peat layer on the bottom; however, pond B lacked macrophytes. Natural lakes covered with free-floating vegetation were very similar to pond A, but these water bodies showed a lower temperature, dissolved oxygen level and pH and a higher conductivity than the non-vegetated pond. Our results indicated that water hyacinth has a strong local influence on the limnological conditions in subtropical shallow lakes. Our results may assist in developing cause-consequence models by demonstrating the relevance of the effect of thermal damping produced by floating meadows.