Ensuring forest protection and the delivery of forest ecosystem services is a central aim of the European Union’s biodiversity strategy for 2020. Therefore, accurate modelling and mapping of ecosystem services as well as of biodiversity conservation value is an important asset in support of spatial planning and policy implementation. The objectives of this study were to analyse the provision of the multiple ecosystem services under two forestation scenarios (eucalyptus/pine vs. oak) at the watershed scale and to evaluate their possible trade-offs with the biodiversity conservation value. The Vez watershed, in northwest Portugal, was used as case study area, in which soil and water assessment tool (SWAT) was applied to simulate the provision of hydrological services, biomass and carbon storage services. Biodiversity conservation value was based on nature protection regimes and on expert judgement applied to a land cover map. Results indicated large provision of ecosystem services in the high and low mountain sub-basins. The overall performance for water quantity and timing is better under the shrubland and oak forest scenarios, when compared to the eucalyptus/pine forest scenario, which perform better for flood regulation and erosion control services, especially in the low mountain sub-basin. The current shrubland dominated cover also shows good performance for the control of soil erosion. The oak scenario is the one with less trade-offs between forest services and biodiversity conservation. Results highlight SWAT as an effective tool for modelling and mapping ecosystem services generated at the watershed scale, thereby contributing to improve the options for land management.