Recent studies on decentralized wetland governance in Uganda have focused mainly on the relationship between central and local governments. Less attention has been given to the relationship between agricultural systems, local governments, and water bodies. This study aims at assessing decentralized wetlands governance in the upper river Rwizi and Iguluibi micro catchments, Lake Victoria Basin Uganda, in relation to farming practices. Qualitative and quantitative methods were used to provide a comprehensive understanding of the contribution of decentralized governance to the management of wetlands resources. Quantitative survey data were analyzed using descriptive summary statistics with the help of Statistical package for Social Sciences (SPSS) soft ware. Qualitative data analysis involved the categorization of verbal and behavioral data for purposes of classification with the use of Nvivo soft ware. Data were analyzed at two levels: the descriptive level of analysis which is the account of the data in terms of what was said, documented or observed with nothing assumed about it. The second level of analysis was interpretive, where data is transformed into what is meant by the responses and conclusions are drawn. All recorded interviews were transcribed into a written report. Findings revealed that decentralized wetlands governance has brought ecosystem services nearer to communities in form of community-based management planning. However, results indicated inadequate institutional capacity, knowledge gaps of existing legal frameworks, limited political support and accountability for local leaders, lack of cooperation and coordination, and inadequate funding. In all, the policy has not fully realized its intended outcomes.