The participation of indigenous communities and use of indigenous knowledge systems (IKS) in environmental governance is provided for in several international and national environmental legislation and policies. In South Africa, the National Environmental Management Act 107 of 1998 (NEMA) in Chapter 1, Principle 4g requires that decisions must take into account the interests, needs and values of all interested and affected parties, and this includes recognising all forms of knowledge, including traditional and ordinary knowledge. This study investigated the Environmental Impact Assessment process (EIA) in mining developments in three rural communities in Limpopo Province, South Africa with regards to the effectiveness of public participation in fostering the incorporation of IKS. The qualitative research design used in this study employed several research methods through the utilisation of 3 villages as a case study. Semi-structured interviews, a focus group discussion and document analysis were used to collect information regarding the public participation process and the integration of IKS into EIAs. This report illustrates that IKS exists in rural communities and some of it is relevant to be incorporated in EIAs. This research study has shown that while expert knowledge dominates the EIA process, there is no indication that this is done deliberately to exclude IKS. This study has also revealed that the public participation process has a number of weaknesses such as in the selection and composition of community stakeholders and communication procedures. Suspicions also developed amongst the villagers of community representatives being bribed by the mine, and infighting started within community committees resulting in some community members losing trust in the committees. The disagreements with regards to the integrity of community committees created divisions and this negatively impacted on the public participation process. However, despite these weaknesses, if capacity building for both EIA experts and rural communities is done, the public participation process has potential as a tool to aid the integration of IKS into EIAs.