The Little Ice Age (LIA - A.D. 1400 to 1820, 550 to 130 cal yr BP) was a significant worldwide climatic fluctuation, yet little is known about its impact on the ecology of Amazonia or its human inhabitants. Using organic geochemistry and diatoms, we investigate the limnological impact of this event in an Amazonian record spanning the last 760 years. The sedimentary record is from Lake Pata (Lagoa da Pata), which lies on the Hill of Six Lakes (Morro dos Seis Lagos), in the wettest section of the western Brazilian Amazonia. We found that many of the diatom taxa recovered from this remote site are either morphotypes of known species or species new to science. Eunotia and Frustulia dominated our fossil diatom assemblage over time, indicating oligotrophic waters of low pH. The limnological characteristics of this pristine system changed very little over the last millennium, except for a slight intensification of precipitation indicated by the increase in Aulacoseira granulata abundances, in C/N ratios, and in sedimentation rates. This phase lasted from 1190 to 1400 A.D. (760 to 550 cal yr BP). Although occurring before the onset of LIA, the observed change matched increases in precipitation observed in Venezuelan glaciers and Peruvian speleothems. We conclude that although the changes in precipitation detected in our lake match the timing of precipitation increase in some South American records, the event was shorter and its effects in this region of Amazonia were mild compared with other regional records. Our paleolimnological data provide additional insights into the interpretation of a remarkably stable fossil pollen record, in that the highest variance in vegetation occurred over the last millennium. Because Lake Pata has no human influence, part of its value is in providing a reference, with which variability in other settings that do have a human history, can be compared.