The European regulation of biodegradable municipal waste (biowaste) treatment places a significant demand on local biowaste separation systems and consequent treatment (composting, anaerobic digestion). When implementing separate collection systems, there is a public demand for systems based on containers and bags. Based on a case study of the city Ústí nad Labem in the Czech Republic, the authors illustrate the difficulties encountered in the implementation of this kind of system. A series of factors should be paramount in the organization of biowaste separate collection, including the location of containers, the amount of contaminants, and system parameters (e.g. volume of containers, frequency of collection). The results obtained confirm how a precision-targeted information campaign may contribute towards reducing contamination of biowaste container content. Lower amounts of contaminants imply a simplified biowaste treatment (composting) and increased system efficiency. Furthermore, it was observed that the relocation of biowaste containers, or placing of additional containers in the system, resulted in an increase in public involvement as a result of the added convenience of separate collection proximity of containers. The equipment of the chosen city district by additional 55 containers increases the number of address points covered by the system by approx. 149.20% and the number of inhabitants by about 38.14%. However, this added convenience of separate collection is not cost-neutral, with the increased proximity of containers contributing towards a rise in collection costs including transport, and containers. The increase of collection costs ranges between 105.5 and 156.78% in comparison with the current situation.