This paper analyses waste management on small islands (on a global scale these are micro-islands). In the context of the paper, small islands are islands that have an area less than 50 km². The study presents an overview of the problems connected with waste transport from islands to the mainland. Waste generation on islands is very much related to tourists. If tourists do not handle waste properly, it will cause problems. Four small Estonian islands in the range of 3–19 km² are studied in detail. For these and other small islands, the main problem is the waste produced by tourists, or related to tourists and waste transport to the mainland. Currently, the local municipality has to arrange and finance waste transport. In fact, and based on the polluter-pays principle, the tourists should bear the cost of waste management. There are different tax options available in order to collect the money from tourists – waste tax, harbour tax, tourist tax, donations, environmental tax and others. The study results revealed that the best possible solution for Estonian islands may be a non-deposit system – including an additional charge on ferry ticket prices. The extra money should cover the costs of waste management and waste shipping. The tourists arriving in their own boats should pay a harbour tax, which includes a waste tax to compensate for the cost of waste management.