The dentification of nursery areas is a basic requirement for fishing management in large rivers. Morphometry (circularity, ellipticity, form factor, rectangularity and roundness indices) and chemistry (Sr:Ca, Ba:Ca and Zn:Ca ratios) of lapilli otolith, and geometric morphometry of scales of juveniles Prochilodus lineatus , were compared in three sites in the Plata Basin, in order to evaluate their applicability to identify possible nursery areas. Otolith microchemistry based on ICP-OES found significant differences in the Ba:Ca and Zn:Ca ratios among sampling sites. When all the combined techniques were considered, the quadratic discriminant analysis (QDFA) showed the highest classification success (89.5–92.9%), in relation to separate techniques classification. Otolith microchemistry, individually considered, appears to be a good and effective tool to identify individual fish from different locations (77.8%–84.2%). Otolith morphometry found significant differences in the ellipticity, circularity and form factor indices between sites. Otolith morphological indices supported results from the elemental study with a success in the allocation of 63.2–78.6%. When considering all variables for scale geometric morphometry, discriminant analysis showed a good percentage of the classification of the individuals (58.3–82.8%). These results indicate that the otolith microchemisty and morphometry and scale morphometry are acceptable markers of habitat and represent a potential tool (in combination or individually) for the identification of streaked prochilod nursery areas. [ABSTRACT FROM AUTHOR]