Marine coastal habitats are being increasingly impacted by human activities. In addition, there are dramatic climatic disruptions that could generate important and irreversible shifts in coastal ecosystems. Long-term monitoring plays a fundamental and irreplaceable role to establish general baselines from which we can better address current and future impacts and distinguish between natural and anthropogenic changes and fluctuations. Here we highlight how over 25 years of monitoring the coastal marine ecosystem within the no-take marine protected area of Las Cruces has provided critical information to understand ecological baselines and build the necessary ecological literacy for marine management and conservation. We argue that this understanding can only be gained with simultaneous monitoring of reserves and human-impacted areas, and the development of complementary experimental studies that test alternative hypothesis about driving processes and mechanisms. In this contribution we selected four examples to illustrate long-term temporal fluctuations at all trophic levels including taxa from algae to sea birds. From these examples we draw a few general lessons: a) there is co-occurrence of rapid- and slowly- unfolding ecological responses to the exclusion of humans within the same rocky shore community. The sharp differences in the pace at which depleted populations recover is at least partly related to differences in life history (dispersal capabilities) of the targeted species. b) Long-term monitoring of the supply-side of marine communities is critical to evaluate the potential feedback effects of local changes in abundance into the arrival of new individuals and to correctly evaluate environmental and human-induced perturbations. c) Unexpected changes in local population dynamics can occur in independent and apparently non-interactive modules of the marine ecosystem, such as roosting sea birds inside the reserve. In addition we discuss the way in which ecological data generated from long-term monitoring at marine reserves was institutionalized in a national marine management policy. At the same time, we highlight the mismatch between the gained scientific information and principles from these studies and the current concept of marine protected areas that is being implemented by some government agencies in Chile. Information from long term monitoring programs has proved essential to understand how marine environments respond to anthropogenic and/or natural disturbances, however funding these schemes, which generally have no short term gains for funding agencies in both developing and developed countries, still remain a major challenge.