This paper brings some advances in fish data sampling and stream environments. Since the publication in 1999 of volume VI “Ecology of Stream Fishes” in the former Oecologia Brasiliensis journal, today Oecologia Australis, several progresses have occurred. Several methods of collecting fish themselves, have remained the same. However, in relation to the use of electric fishing, collection of eggs and fish larvae, and characterization of physical habitats in streams, there was remarkable development and improvement. The purpose of this article is to present the “state of the art” of these three aspects of sampling fish and habitats in streams. By the end, preparation methods of samples for genetic, stable isotopes and heavy metal analyses are briefly presented