This dataset represents metadata from the paper Yunoki, T. and Torres, L. V. (2015): The role of water chemistry, connectivity and piscivory for ecological and evolutionary process structuring a fish metacommunity in the Bolivian Amazonian lowland. This study documents the spatial dynamics of fish metacommunity based on the dataset of 65 sites in two geographic patches of transparent black and clear waters of the Amazonian Manuripi and Itenez Rivers, which are separated by river valleys with turbid waters originating in the Andes and the savanna. More information on this dataset can be found in the Freshwater Metadatabase - BFE_105 (http://www.freshwatermetadata.eu/metadb/bf_mdb_view.php?entryID=BFE_105).