Creating protected areas (PAs) intended to counteract the effects of human activities on the environment is a significant step towards conserving coastal and marine ecosystems. Various countries have introduced legal mechanisms to create and manage their important ecosystems, such as mangroves. Despite the significance of evaluating the effectiveness of PAs, literature on the topic is scarce, especially pertaining to the mangrove ecosystems. Therefore, the present study intended to evaluate the management of a PA located in northeastern Brazil throughout the first decade of the current century (2003, 2006, and 2012). The management of the PA was considered inadequate, and the level of efficacy even declined progressively, although a slight improvement was recorded in 2006. The respective levels of effectiveness were 35%, 50%, and 15% for 2003, 2006, and 2012. The improvement recorded in 2006 was attributed to a new management plan and the ensuing environmental actions, such as monitoring and management programs, PA zoning, and others. The worst management performance was indicated for the following assessment parameters, namely, administrative matters (public administration), biogeographic characteristics, and threats. One of the main reasons for the low management effectiveness is that the mangrove PA is located in an urban area of one the most densely populated cities in Brazil, namely, Fortaleza, (7786 inhabitant/km2). The location has led to an increase in the number of threats to the PA and has strongly influenced the biogeographic characteristics. The urbanization in and around the area has resulted in the PA being isolated, with no connection to other ecosystems through ecological corridors. Both direct measures and strategic planning are required to facilitate continuous improvement of the management effectiveness of PAs. This strategy is imperative in countries with tropical ecosystems characterized by significant biodiversity, which is vulnerable to anthropogenic effects.