In recent years increasing attention has been given to the potential use of contaminated lands for biofuel production, because these degraded soils cannot be used for food production. To establish these crops in Mediterranean contaminated areas, where the soil quality is usually very poor, the addition of soil amendments might be necessary to improve soil productivity. In addition, the use of crops with low water demands, adapted to these particular conditions of climate and soil contamination, is a key requirement. We studied the development of Cynara cardunculus and Silybum mariamun crops (both suitable for the production of biomass for biofuel uses under a Mediterranean climate) in trace element contaminated soils under field conditions. To our knowledge, this is the first such work under these particular experimental conditions (soil contamination and field trial). Soil physical (hydraulic), chemical, and biochemical properties were monitored for one year in experimental plots, where we tested the effects of the addition of two different amendments (sugar lime and biosolid compost) on soil functioning and crop productivity. Seed germination and plant biomass production were low, although amendment addition improved both parameters. The chemical and biological indicators (enzyme activities, PLFA profiles, and soil respiration) tended to be slightly improved by the amendments, especially sugar lime. The hydraulic properties of the soil in the experimental area were very deficient, and the effect of the amendments was not enough to improve them; this was probably the main cause of the general low productivity of these rain-fed crops, as water infiltrated poorly through the root zone. To improve crop productivity under these soil conditions, certain aspects could be improved: higher doses of amendments should be applied and deeper tillage of the soil after amendment addition should be performed to facilitate water infiltration.