In our research 20 benthic samples were collected from small rivers and streams from industrial and nature areas of Novosibirsk region. Benthic invertebrates were fixed at 75% ethanol and identified up to the family taxonomical level at the laboratory. Samples were dried up to stable weight, animals from each taxonomical group were placed at the conductive tape for further investigation. The analysis was carried out using the μXRF-SR according to the standard certified method at the experimental station "Elemental analysis" in the SCSTR (Budker INP SB RAS). Experimental conditions: excitation energy 21 keV, dimensions of the exciting radiation beam 0.5 mm in height and 10 mm in width of the sample. Measuring time for one point was 100 s. The contents of more than 20 elements, including essential Cl, K, Ca, Mn, Fe, and trace elements Ti, V, Cr, Ni, Cu, Zn, As, Rb, Sr, Y, Zr, Nb, Mo, Pb were determined. The concentration range for essential elements was 150-500000 ppm, for trace elements 0.3-15000 ppm. Scanning was done in two directions - the length and width of the sample animal. The profile of scanning was compared with photos from the electronic microscope. That gave us an opportunity to find out a specific locus of accumulation of some elements. Results obtained shown patchy spreading distribution of elements in the samples, that could be interpreted by various forms of chemical compounds, which included explored elements. For more complete result 3d scanning with the function of focused X-ray optics could be used.