Although it boasts a rich historical wealth of traditional ecological knowledge, the rural Eastern Cape of South Africa continues to be an environmental hotspot since the mid-twentieth century, suffering land degradation, overharvesting of resources and water scarcity. Over the years, much research effort has been directed to investigating how local communities use traditional knowledge to manage resources. By and large, the studies argue that traditional knowledge provided effective management strategies in the past, hence communities should continue using it. This raises the question: what is happening with traditional ecological knowledge in contemporary rural Eastern Cape in South Africa? To address this question, this work used snowball sampling to recruit 83 respondents from three villages of Colana, Gogela and Nozitshena for in-depth interviews. The respondents were elderly women and men whose families had at least a two-generation history of living in these villages. Using the meta-theory of critical realism, particularly its analytical tools of abduction, hermeneutics, dynamism and context, this work found that there are multiple factors, exogenous to traditional ecological knowledge, that make it fail to effectively address environmental challenges in the present-day rural Eastern Cape. They include changed worldviews, legal pluralism and changed lifestyles which are a consequence of adverse incorporation of traditional systems into the South African nation-state system. Indigenous practices, traditions, local ethics, taboos, social conventions, and other cultural practices, that ensured the usefulness of TEK, have been abandoned over time. Incorporation of rural traditional systems into the South African nation-state have been largely adverse. There has been little or no integration of TEK and the “imported” lifestyles. The application of the “plug-in” principle in this case, thus, faces a very formidable task despite the reality that it is the way to go to ensure sustainable natural resources management and the achievement of some of the SDGs.