|Although an integrated approach that combines modern and indigenous knowledge is critical in the attainment of environmental sustainability, a framework to facilitate the same needs to be designed for Teso District. To contribute to this need, this study assessed the effects of changes in indigenous environmental knowledge systems on the bio-physical environment and community livelihoods between 1960s and 2000s with the ultimate aim of providing building blocks for the intended framework. The study targeted household heads in general and the Teso Sages aged 70 years and above because of their wealth of experience and knowledge in the community‟s indigenous knowledge. A sample size of 384 respondents was used. Data were collected using a variety of social science research instruments such as structured questionnaires, in-depth face-to-face interviews, focussed group discussions, content analysis of literature and environmental check lists. The status of the bio-physical environment was tracked using GIS techniques. Questionnaire data were subjected to descriptive statistical analysis using SPSS. Results showed that adherence to the Teso community indigenous environmental management systems has been on the decline since the 1960s. Use of traditional terracing, grass-strips and fallowing have declined by 54%, 61% and 74%, respectively. Also use of totems, protection of sacred places, prohibitions and gender and age restraints have declined by 41.3%, 68%, 41.8% and 38.2% , respectively. The evident decline in the use of the indigenous environmental knowledge systems has negatively impacted on the state of the bio-physical environment and community livelihood as exemplified by the Chi-square Pearson (P) values of 0.00 between decline in the use of age and gender restraints and the deterioration in land fertility, 0.003 between a few elders using indigenous knowledge systems and increased cost of living as well as 0.001 between only a few elders using the knowledge systems and increased morbidity and mortality leves from the 1960s to the 2000s era. GIS results showed evidence of environmental changes such as an increase in land size under rain-fed agriculture by 11.2% and a decline in land under seasonal swamps by 21% between 1973 and 2010. Land size under wetlands dropped by about 33% between 1973 and 2000. These changes were indicative of the declining ability of indigenous systems to protect and conserve these resources. As a final output, an integrated environmental management framework for Teso was developed. Its main building blocks are (i) partnership engagements, (ii) Scientific and community problem analysis, (iii) Scientific and community points of convergence and divergence (iv) community and expert based resolutions (v) community-based project implementation monitoring and evaluation. The study findings showed that indigenous beliefs and best practices with proven utility are still capable of enhancing environmental management (use, care and improvement); and also the community livelihood among rural communities such as the Teso. In view of the above, it is recommended that rekindling, recording and preservation of indigenous environmental best practices among local communities such as the Teso for sustainable natural resources management be re-invigorated and integrated in conventional environmental management plans. This also calls for participatory decision-making between policy makers, implementers and actual resource users.