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Species of Pseudotocinclus are found in the upper Tietê River basin in the ribeirão Grande, a tributary of the middle course of the rio Paraíba do Sul, Pindamonhangaba, in the headwaters of rio Itatinga, a coastal river of São Paulo, and in the upper and lower courses of the Juquiá River of the Ribeira de Iguape River basin, all rivers of São Paulo, Brazil.
P. juquiae has also been found in the ribeirão Poço Grande, a tributary on the right margin of the Juquiá River; this locality, an old swamp area near the city of Juquiá, is heavily impacted by human activities, and is also used for garbage and sewage disposal.