In Nitrate Vulnerable Zones (NVZ), the impact of animal effluent management on soil fertility is essential. A three-year study was carried out in a NVZ (Arborea, Central-western Sardinia, Italy), aiming to analyze the effect of different fertilization systems on soluble and total soil organic matter (SOM) within a silage maize-hay crop cropping system on sandy soil (Oxyaquic Xeropsamment). Four types of fertilization systems were compared: (i) cattle manure; (ii) cattle slurry; (iii) mineral; (iv) slurry + mineral. The water-extractable C and N content (WEC and WEN) from the topsoil (0–20 cm layer, the Ap1 horizon), the dissolved carbon (DC) and the dissolved nitrogen (DN) of the soil solution collected by disk lysimeters placed along the soil profiles, and the C content at the beginning and at the end of the experiment were determined.The seasonal dynamics of WEC in the topsoil seemed mainly associated with the timing of the fertilizer distribution. In the topsoil, WEC was larger under slurry than under mineral treatment. The DC was rather low in the deeper soil layers and did not show any variation due to the fluctuations of fertilizer distribution that were seemingly influenced by the groundwater table. The fertilization systems influenced the soil C inputs and, in turn, the SOM content. Manure promoted a higher C stock in the deeper soil layers among the organic fertilizers. However, the hay crop added with manure and slurry showed lower crop residues and, thus, C input than that added with mineral fertilizer. This result suggests that the management of these organic fertilizers should carefully consider their impact on the overall productivity of the studied cropping system in Mediterranean NVZ to avoid a potential limitation for soil C accumulation in the long term.