The ever-increasing interest in mining of sand in shallow waters of many rural rivers on the one hand and the growing concern for the environment on the other underscore the need to develop better management policies that govern sand extraction. Although literature pointing to increased environmental consciousness by some mining operations exists, the link between environmental concerns and sand mining has however remained a controversial matter and an under-researched area in South Africa. Consequently, decisions relating to what actions should or should not be taken to limit environmental concerns associated with sand mining operations in South Africa are not known. This analysis sought to explore regulatory and policy implications of sand mining operations along a sample of sites of Njelele River in South Africa. Data were gathered through observation, household questionnaire survey and a series of Participatory Rural Appraisal (PRA) exercises conducted with selected community members and sand miners. We used a combination of K-means clustering and Discriminant Function Analysis (DFA) to determine the major environmental attributes explaining the state of affairs in sand mining. Regulatory and policy implications were developed using a combination of Gap analysis; Strengths, Weaknesses, Opportunities and Threats (SWOT) analysis; and the development of a Threats, Opportunities, Weaknesses and Strengths (TOWS) matrix strategy. Our analysis identified a series of morphological, ecological, socio-ecological, governance and physical factors that were major areas of concern in three distinct clusters of sand mining sites. We concluded by discussing a number of regulatory and policy implications of sand mining at three scales, namely strategic, institutional and operational scales.