An important, although insufficiently answered, environmental governance research question concerns how exactly participation improves policy implementation at different scales. Numerous studies have highlighted important variables influencing the effectiveness of participatory processes. However, studies of participation tend to be strongly process‐oriented rather than system‐oriented and often overlook the reality that participatory processes are part of increasingly complex and broader decision‐making systems. By analyzing particular process‐system linkages, this paper contributes new knowledge regarding how participatory processes can influence decision‐making in polycentric governance systems. This study focuses on the implementation of the EU Water Framework Directive, which aims for good ecological and chemical status in all European waters, in six German states with varied polycentric decision‐making structures. No direct decision‐making power was found to be associated with any of the participatory processes themselves. Rather, the power remained embedded within the other established institutional structures. Nevertheless, the participatory processes did still intend to influence decision‐making within those established structures through the aggregation and multiplication of information. The findings show that only a few representatives or a small proportion of the total number of decision‐makers are involved in participatory processes. Therefore, those processes may either affect decisions directly due to the binding nature of the decisions taken within participatory processes or alternatively have effects through more complex and nuanced multiplication routes following the conclusion of each participatory process. Moreover, all of the participatory processes examined in this study were reliant to some extent on such multiplication mechanisms to amplify the effects on decisions throughout the overall polycentric governance system.