Concentrations of major and trace elements in freshwater fauna are often a reflection of local sediment chemistry. Biogeochemical profiles of freshwater species can be used to provide accurate and affordable assessments of species distribution, movement, and connectivity within river systems. Incorporating additional elements could significantly increase the precision and accuracy of population discrimination and movement analyses. To increase the variety of elements in biogeochemical tracing studies, we compared the concentrations of 38 major, trace, and rare earth elements (REEs) in bulk sediment (< 10 μm) and atyid shrimp from three rivers in South East Queensland, Australia. We determined which elements were correlated between sediment and shrimp samples and if these elements could distinguish different sample populations. This process identified elements that can directly associate shrimp with local sediment geochemical profiles. We found potassium (K), aluminum (Al), yttrium (Y), and the REEs cerium (Ce), lanthanum (La), and samarium (Sm) were spatially correlated between shrimp and sediment samples. Concentration ratios indicated K may be a relatively conservative tracer. Aluminum, REEs, and Y may undergo characteristic fractionation between sediment and shrimp tissue. Multivariate analysis indicated these elements could distinguish shrimp populations between sample sites. Results suggest that this small number of elements can link shrimp with specific rivers in accordance with local geochemistry, and thus may be valuable tracers with which to distinguish freshwater populations. As we measured bulk sediment concentrations, sampling these tracers is a relatively simplistic process that could be applied in a range of field conditions.