Water governance occurs at multiple levels, from the local to the supra-national, which are often highly fragmented. The interconnected nature of water requires interactions among these multiple governance levels. Public participation may foster such interactions. Thus, many water management reforms involved decentralization and public participation worldwide over the last decades. Yet, it is not demonstrated how these reforms may improve water resources sustainability. Their analysis in the literature does not show concretely how interactions among multiple levels materialize and are influenced by participation. As such, the question addressed is how interactions among multiple levels of water governance manifest over time in a participatory intervention. Using a case study in the Rwenzori region in Uganda, this article compares the multi-level interactions before and during a participatory process. The latter has been purposely implemented to bridge gaps between local and provincial levels through a participatory planning process centred on the provincial level. Four types of flows were analyzed: information and knowledge, hydrosocial, financial and human. Our analysis shows that using artefacts like the role-playing game and planning matrix fostered bi-directional information and knowledge flows. Hydrosocial flows did not change in depth but the legitimacy of the two organizations implementing the participatory process was reinforced. Project financial flows were injected through a provincial academic institution, who is not a regular budget recipient. They were therefore superimposed on existing budgeting process. We conclude by providing suggestions for the engineering of participatory processes in order to foster more collaborative and effective multi-level water governance.