Variation in water colour is a remarkable characteristic of Amazonian rivers and reflects their limnological properties and the geomorphology of sub-basins. We present here a literature-based study to examine the relationships between fish species turnover and abiotic properties of Amazonian rivers with contrasting water colours. We analysed fish records and water physicochemical properties (pH, colour, turbidity, dissolved oxygen, ammonia and suspended solids) of eight Amazonian rivers with white-, black- and clearwaters. Rivers with similar water colour shared more fish species than those that contrasted in colour. Increased differences in abiotic parameters imply an increased dissimilarity in fish species composition. Species composition is also related to distance among rivers with high dissimilarity observed in rivers distant to each other. The fish species turnover could be ultimately driven by the geological history of rivers which provides different opportunities to speciation and biotic interchange. Water types likely influence species turnover by selecting fishes with different limits of physiological tolerance and specialized use of different habitat types. Our findings suggest that river water colours are reliable proxies for historical and ecological mechanisms affected fish species distribution. Antropic disturbances of Amazonian rivers with distinct water colours could threaten unique fish assemblages.