Since modern waterway networks are increasingly confronted with ageing assets, waterway renewal will increase in importance for western countries. Renewal can be regarded an impetus for realising integrated waterway networks that internalise externalities, which entails broad stakeholder involvement. This can be coordinated through different inter-organisational structures. Applying a transaction-cost perspective, we contribute to the assessment of effective governance arrangements for renewing waterway networks in such an integrated fashion. Our aim is to examine efficient inter-organisational structures for waterway renewal, as perceived by actors involved in a case study of the Dutch waterways. Our findings show that waterway renewal incorporates additional functionalities in terms of capacity (expansion or reduction), but not so much in terms of quality (combining transportation aims with spatial objectives such as ecology or regional development). Inter-organisational structures that address geographical interrelatedness and, hence, broader stakeholder involvement were associated with uncertain and time-consuming transactions, because of extensive negotiations regarding the alignment of conflicting interests and the crossing of geographical and administrative boundaries. Also, a change in interdependency from hierarchical towards contractual relationships was required, putting dominant actors (the national government) in an unfamiliar position in which they loosen their grip on infrastructure investments. Perceptions on transactions centre on sectoral aims and individual assets, whereas the actual transaction may be different if a perspective is taken that includes the greater waterway system, the wider spatial surroundings and a longer-term horizon. We conclude that short-term, transportation objectives overrule longer-term, integrative objectives, which withholds strategic considerations required for aligning waterway interests.