This work presents an automatic procedure to quantify dune dynamics on isolated barchan dunes exploiting Synthetic Aperture RADAR satellite data. We use C-band datasets, allowing the multi-temporal analysis of dune dynamics in two study areas, one located between the Western Sahara and Mauritania and the second one located in the South Rayan dune field in Egypt. Our method uses an adaptive parametric thresholding algorithm and common geospatial operations. A quantitative dune dynamics analysis is also performed. We have measured dune migration rates of 2–6 m/year in the NNW-SSE direction and 11–20 m/year NNE-SSW for the South Rayan and West-Sahara dune fields, respectively. To validate our results, we have manually tracked several dunes per study area using Google Earth imagery. Results from both automatic and manual approaches are consistent. Finally, we discuss the advantages and limitations of the approach presented.