The influence of manure and composts on the leaching of heavy metals from soil was evaluated in a model lysimeter experiment under controlled conditions. Soil samples were collected from experimental fields, from 0- to 90-cm layers retaining the layout of the soil profile layers, after the second crop rotation cycle with the following plant species: potatoes, spring barley, winter rapeseed, and winter wheat. During the field experiment, 20 t DM/ha of manure, municipal sewage sludge composted with straw (SSCS), composted sewage sludge (SSC), dried granular sewage sludge (DGSS), “Dano” compost made from non-segregated municipal waste (CMMW), and compost made from municipal green waste (CUGW) was applied, i.e., 10 t DM/ha per crop rotation cycle. The concentrations (μg/dm3) of heavy metals in the leachate were as follows: Cd (3.6–11.5) < Mn (4.8–15.4) < Cu (13.4–35.5) < Zn (27.5–48.0) < Cr (36.7–96.5) < Ni (24.4–165.8) < Pb (113.8–187.7). Soil fertilization with organic waste materials did not contaminate the percolating water with manganese or zinc, whereas the concentrations of the other metals increased to the levels characteristic of unsatisfactory water quality and poor water quality classes. The copper and nickel content of percolating water depended on the concentration of those metals introduced into the soil with organic waste materials. The concentrations of Cd in the leachate increased, whereas the concentrations of Cu and Ni decreased with increasing organic C content of organic fertilizers. The widening of the C/N ratio contributed to Mn leaching. The concentrations of Pb, Cr, and Mn in the percolating water were positively correlated with the organic C content of soil.