Pumping and tracer tests are common methods for the characterization of the aquifers used for supplying desalination plants. A case study is presented from Almería in SE Spain in which the unexpected movement of fine sediment caused by continuous pumping and incomplete removal of the drilling mud in the boreholes makes it impossible to conduct and interpret a standard tracer test. A modified tracer test was therefore performed in the unconsolidated clastic aquifer at this site and then interpreted numerically using two conceptual models: (1) a homogeneous model representing an unaltered medium; (2) a heterogeneous model incorporating an alteration zone around the borehole. The heterogeneous model produced a better calibration with more realistic parameter values for the aquifer and silty material (permeability, specific storage, effective porosity, dispersivity). The aquifer was characterized as a poorly sorted detrital sedimentary deposit with a large quantity of silt in the matrix. The conclusion is that advective transport dominates almost all the tracer movement. However, dispersive and/or diffuse transport determine the tail length of the breakthrough curve.