ABSTRACT Limnological characteristics of the Violão and Amendoim lakes, in the Serra dos Carajás, Amazon, were studied interannually (2013-2014). Climate data indicate anomalous conditions during the 2013 rainy period with higher rainfall and lower temperature in the beginning (November). Lake levels were influenced after the first and second hour of each rainfall, which showed a strong synchronization between seasonal fluctuation of lake levels and local weather patterns. Based on the water quality, both lakes are classified as classes "1" and "2" in the CONAMA (Conselho Nacional do Meio Ambiente) scheme and as "excellent" to "good" in the WQI (Water Quality Index) categories. However, the limnology is distinctly different between the lakes and seasons. Higher trophic state and phytoplankton productivity were observed mainly during the rainy period in Violão Lake compared to Amendoim Lake. This may be due to deposition of leached nutrients in the former, mainly total phosphorus (TP), which was probably derived from mafic soils and guano. This is consistent with the significant positive correlation between Chlorophyll-a and TP at the end of the rainy period (March-April), whereas this was not observed in the beginning (November). This could possibly be a consequence of the more intense cloud cover, and unusual high rainfall that limits nutrient availability.