In this paper we focus on systemic delays in the Baltic Sea that cause the problem of eutrophication to persist. These problems are demonstrated in our study by addressing three types of delays: (1) decision delay: the time it takes for an idea or perceived need to be launched as a policy; (2) implementation delay: the time from the launch of a policy to the actual implementation; (3) ecosystem delay: the time difference between the implementation and an actual measurable effects. A policy process is one characterized by delays. It may take years from problem identification to a decision to taking action and several years further for actual implementation. Ecosystem responses to measures illustrate that feedback can keep the ecosystem in a certain state and cause a delay in ecosystem response. These delays can operate on decadal scales. Our aim in this paper is to analyze these systemic delays and especially to discuss how the critical delays can be better addressed in marine protection policies by strengthening the adaptive capacity of marine protection. We conclude that the development of monitoring systems and reflexive, participatory analysis of dynamics involved in the implementation are keys to improve understanding of the systemic delays. The improved understanding is necessary for the adaptive management of a persistent environmental problem. In addition to the state of the environment, the monitoring and analysis should be targeted also at the implementation of policies to ensure that the societies are investing in the right measures.