Plastics are widely used in agricultural practices, although recently they have been recognized as a new emerging risk in soils. Polyethylene (PE), is commonly used by farmers to cover agricultural practices; geotextile, is used mainly for ground and crop covering; and polyvinyl chloride (PVC) is considered the main material contained in irrigation hoses. The present study aimed to assess the effects of three plastics (polyethylene, geotextile, polyvinyl chloride) on the soils’ fertility. Several pot experiments were conducted in soil samples from the study area (Thessaly) contaminated with adequate amounts of each plastic type (PE, geotextile: 2% v/v and PVC: 5% v/v). Water was added in two quantities: one to maintain typical soil moisture levels according to the crops’ requirements and an elevated amount to form supersaturating soil conditions similar to those following a flood event. Furthermore, temperature effect was also investigated to assess its impact on plastics’ behavior and soil fertility. The levels of all nitrogen forms and the microbial activity were determined at 10, 30, and 60 days. Significant changes were observed in the concentrations of nitrate, nitrite, and ammonium ions under ambient soil moisture conditions especially when the microplastics were incubated for a longer period. PE addition resulted in greater changes, followed by geotextile, although PVC addition did not induce significant changes in the nitrification process during the experimental time. PE and geotextile microplastics appeared to enhance microbial colonization and total microbial activity. In addition, soil characteristics were notably altered when moisture stress conditions were reached (85%) and when soils were flooded for two months, leading to a severe decrease in the availability of all nitrogen forms. The results showed that alterations in soil nitrogen forms in the presence of plastics study are crucial for maintaining the health and improving the productivity of Mediterranean soils.