The European Union set in place Directive 2000/59/EC with the aim of substantially reducing discharges of ship-generated waste into the sea by improving the availability and use of port reception facilities. According to the Directive, port administrations shall ensure that the cost recovery system must aim to discourage ships from discharging their waste into the sea, while simultaneously placing the burden of costs on ships, in line with the "polluter pays principle". The present paper examines the extent to which the deposit-refund framework could be used in charging systems of port reception facilities. This has been realized through a case study involving a Greek port. Specifically, the charging system proposed here seems to approach quite close to the primary target, i.e. to a charging system that motivates ships to act more environmentally responsible manner regarding their waste, without significantly affecting their total cost nor the competitiveness of the port.