In this study, composites containing polylactide and carbonate lake sediment in concentrations of 2.5, 5, 10, and 15% by weight were prepared by a 3D printing method. The material for 3D printing was obtained by directly diluting the masterbatch on an injection moulder to the desired concentrations, and after granulation, it was extruded into a filament. The material prepared thusly was used to print standardised samples for mechanical testing. To compare the mechanical properties of the composites obtained by 3D printing and injection moulding, two sets of tests were performed, i.e., mechanical tests (tensile strength, flexural strength, and impact strength) and hydrophobic–hydrophilic surface character testing. The degree of composite waste in the 3D printing was also calculated. Mechanical and surface tests were performed for both systems conditioned at room temperature and after accelerated ageing in a weathering chamber. The study showed differences in the properties of composites obtained by 3D printing. Sedimentary fillers improved the hydrophobicity of the systems compared with pure PLA, but it was not a linear relationship. The PLA/CLS sedB composite had higher strength parameters, especially after ageing in a weathering chamber. This is due to its composition, in which, in addition to calcite and silica, there are also aluminosilicates, causing a strengthening of the PLA matrix.