Aim: Conservation management in freshwater systems requires addressing some key ecological processes to warrant functional and effective protected areas. There are systematic planning methods available to address these needs, but they often result in large areas identified as priority for strict protection, which might constrain their implementation. Considering multiple zones with different management regimes might provide a more flexible and practical solution to this problem, though this approach remains poorly used in freshwater systems. We evaluate the use of a multizone approach to enhance protection of freshwater biodiversity and ecological processes in a large reserve network, Natura 2000.

Location: Iberian Peninsula.

Methods: We tested three scenarios of freshwater conservation planning: (1) a protection‐only approach based on areas identified using Marxan; (2) a more flexible approach where multiple management zones are considered using Marxan with Zones, both accounting for Natura 2000; and (3) a third one similar to (2) but ignoring Natura 2000. The three scenarios were compared considering their effectiveness in representing all species. We also evaluated the role of Natura 2000 within the management zones identified and the effect of these areas.

Results: We found that although there was only an 8% reduction in total area required to complement Natura 2000 under the multizone approach compared to the protection‐only approach, the refinement of conservation recommendations under different management zones can reduce the area needed for strict protection by 62%. Considering Natura 2000 compromised the efficiency of solutions while only one‐third of its extent was selected under the strict protection zone.

Main conclusions: The refinement in management recommendations and resulting improvement in efficiency achieved by using the multizone approach could help unlock the needed expansion of Natura 2000 to adequately cover freshwater conservation needs in the Iberian Peninsula and other areas where similar issues have been highlighted.