Conserving biodiversity with a growing human population is a key sustainability challenge. Consequently, a vast number of development initiatives across the globe have been designed to combine social, economic, and environmental perspectives. For the most part, the development community is well acquainted with the negative experiences and unintended consequences that some projects have or may bring. However, in tropical coastal ecosystems, this aspect is not completely acknowledged, studied, or understood. Here, we use tropical seagrass meadows as a model social-ecological system to investigate how sustainable development initiatives result in unintended consequences with both positive and negative outcomes for environment and society. We analyze the initiatives and their effects in terms of a typology encompassing "flow", "addition", and "deletion" effects and investigate them across four types of sustainable development initiatives that occur within tropical coastal environments: (1) megafauna conservation, (2) alternative livelihood programs, (3) mosquito net malaria prophylaxis, and (4) marine protected areas. Using these four initiatives as examples, we show that sustainable development initiatives can produce unintended effects with major consequences. Further, we illustrate how not assessing such effects may ultimately undermine the initial goals of the sustainable development intervention. Our study suggests that acknowledging unintended effects and transitioning them so that they become sustainable is more effective than ignoring effects or viewing them as trade-offs. We strongly stress the need for an a priori process in which positive effects, negative effects, and potential uncertainties and surprises are considered when planning the development intervention, and we argue for greater social-ecological monitoring of initiatives. As such, this contribution links to contemporary approaches dealing with the sustainability of natural resources and social-ecological systems and bridges with the importance of development initiatives in the context of the United Nations Sustainable Development Goals.