The European Union (EU) has two potentially conflicting policy goals: the Lisbon Agenda and the Cardiff process which, respectively, aim to make the EU most competitive and dynamic knowledge-based economy in the world, and integrate the environment into all EU policies. This research uses two case studies of Operational Programmes drawing on EU structural funds. Such programmes have recently been made subject to Strategic Environmental Assessment (SEA) under the EU SEA Directive, and allowed an assessment of the substantive (does it achieve its goals) and transactive (is it cost efficient) effectiveness of the SEA process, (i.e. does it support the Cardiff process or the Lisbon agenda?). Documentary review and interviews were the primary method drawing on actors involved both in the two case studies, and within the EU. The results indicate that transactive and substantive effectiveness are intrinsically linked and that both cases demonstrated some substantive effectiveness, but only one was transactively effective. Effectiveness was judged to be a function of design, procedure, substance as well as transaction, influenced by political issues. As with other research, we find that perspectives of effectiveness are very much driven by individual expectations, suggesting that a true measure of effectiveness might be the extent to which SEA can change expectations.