European Union (EU) became a party to the United Nations Convention on Law of the Sea (UNCLOS) in 1 April 1998. UNCLOS can generate several and sometimes complicated legal effects with regard to the EU, either partially or fully separate from the EU’s other international agreements, since it is multilateral, have the characteristic of constitution of the seas in substantive terms, brings an institutionalised structure, including International Tribunal for the Law of the Sea, in institutional terms and is a mixed agreement in EU terms. Hence, for these reasons, this Article aims to present the legal effects of the UNCLOS with regard to the EU, on the basis of principle of institutional balance and general effects under EU law, in the light of the case-law of the Court of Justice of the European Union. As will be seen, generally, the principle of institutional balance has been against the maximum control demands of Member States and for the desire of the EU institutions, which bear overriding supranational characteristics, to take the control in their hands in relation to the UNCLOS matters. Besides, both UNCLOS and international customary law as long as composed by a provision of UNCLOS, provided that they are binding on the EU, can be a subject of infringement proceedings and principle of consistent interpretation; however, contain partially certainty, furthermore inconsistencies in relation to directly effectiveness, legality review and EU’s non-contractual liability.