Actors rarely approach institutional design choices with a blank slate but are influenced by design choices made at earlier stages. How does institutional design evolve over time and are there specific paths to deepening cooperation? We investigate the institutional design paths of subnational cooperation that are chosen to address increasingly complex and interconnected policy problems. We theorize that besides the substantive problem, earlier choices matter to explain what institutional design mechanism is chosen; that is, the design of existing institutions between two subnational governance units, called substates, influences the design of subsequent institutions. Using a semi-parametric Cox proportional hazards model, we show that the design paths of subnational cooperation in the Swiss water governance sector correlate with earlier design choices. Our results indicate that not all cooperation is self-reinforcing and path-dependent, but they show which specific design choices are more likely to follow each other in repeated formal federal intergovernmental cooperation.