This paper shows the changes in soil properties in the fourth year after the application of two kinds of environmentally burdensome wastes. One of the wastes was mineral—carboniferous rock from a coal mine, and the other one was organic—post-fermentation sludge from an agricultural biogas plant. The wastes were applied once to a soil of poor quality—a Podzol. The hypothesis to be verified was that one-time application of waste carboniferous rock and/or post-fermentation sludge to a soil has a beneficial effect on the physical status of the soil, and the changes in the soil properties have a permanent character. Also, based on the experiment results, we suggested how these types of waste should be applied to soil. For that purpose, an assessment was performed of the durability, range, and character of changes in soil properties, inter alia: soil texture (PSD), total organic carbon content (TOC), particle density (PD), bulk density (BD), total porosity (TP), air capacity (FAC), air permeability (FAP), sampling moisture (SM), field water capacity (FC), available water (AWC), unavailable water (UWC), and hydraulic conductivity (Ks). Some soil properties have been improved by the use of post-fermentation sludge and the combined application of the two wastes. These were the following soil properties: PSD, TOC, BD, TP, and SM. However, changes to the soil air-water properties (FAC, FAP, FC, AWC, UWC, and Ks) were unfavorable. The effect of the waste’s application was permanent, as differences in soil properties were still visible in the fourth year after their addition. The observations made in the course of the experiment indicate that natural utilization of wastes requires a lot of consideration and should be focused on keeping the balance in the relations between the environmental functions of the soil.