These are the raw data corresponding to the measurement of excitation-emission fluorescence spectroscopy (EEMS) in bile of two species of tropical fish native to the Colombian Orinoquia. The collection of these data is novel to understand the behavior of bile as a reservoir of toxic compounds and to use it to evaluate the environmental risk of organisms exposed to industrial or urban discharges. The data is part of a study funded by Colciencias-ANH and Universidad de los Llanos Project number 112272151869, contract 162-2016, grant 721 – 2015 (“Convocatoria para la formación de recurso humano en Colombia en el área de hidrocarburos, a través de proyectos de investigación”).