During the mining process in mines, a problem arises with the formation of coal post-mining waste, which is waste rock. It is often stored by mines on various types of land to manage the resulting spoil. However, this is not without its impact on the soil. In this study, we determined the biological and physicochemical properties of rhizosphere soils of the podzolic type, subjected to waste rock reclamation and without the influence of waste rock (control), differing in the type of agricultural use and type of plant cover: field-monocotyledonous (oat cultivation), field-dicotyledonous (buckwheat cultivation), and wasteland covered with very species-poor vegetation. Research has shown that long-term cultivation (buckwheat) contributed to the elimination (leveling out) of the microbial and biochemical differences. The addition of waste rock significantly reduced the number of microorganisms synthesizing siderophore, especially on wasteland (decreased by 1.5 log10/gDW). The abundant presence of the genera Acidocella and Acidphilum, absent in wasteland without waste rock, in the unused soil under the influence of waste rock was strongly associated with the effect of lowering the pH by waste rock in soil not used for agriculture. Increased levels of 77 types of bacteria were observed in samples from buckwheat cultivation compared to wasteland. The number of microorganisms resistant to heavy metals as well as microorganisms capable of producing specific Fe-binding ligands—siderophores—decreased under the influence of waste rock. Moreover, the dehydrogenase activity in long-term cultivation both under the influence of waste rock and without its influence was at a similar level. In contrast, an almost 100-fold decrease in dehydrogenase activity was observed in soils with oat cultivation and a more than 4-fold decrease in acid phosphatase (ACP) and alkaline phosphatase (ALP) activity. These parameters provide an effective system for monitoring soil health, from inexpensive and fast methods to advanced and precise techniques. The results can be applied to solve the problems associated with coal mining wastes by developing methods for their use in soils with long-term agricultural use.