The article presents the continuation of the research on modification of fibrous carriers based on poly(lactic acid) using the electrophoretic deposition (EPD) method by the two types of biocompatible polymers—sodium hyaluronate and sodium alginate. Such modified nonwovens, differing in the structural parameters due to different manufacturing methods, could be potentially used in different biomedical applications. The results of the analysis indicate that the EPD process significantly changes the structural characteristics of the carrier in terms of thickness and porosity, which not always can be beneficial in terms of the final application. The varying structure of both carriers significantly influences the mode of deposition of the layer, the efficiency of the deposition process as well as the structural characteristics of the carrier after deposition. Microtomographic and SEM studies were employed to analyze the structure of deposits, and FTIR analysis allowed for confirmation of the occurrence of the polymer layers and its chemical structure.