This SWAT+ modelling protocol was designed for guiding model setup development and model calibration in 14 European case study sites participating in the modelling component of the EU funded research and innovation project OPtimal strategies to retAIN and re-use water and nutrients in small agricultural catchments across different soil-climatic regions in Europe (OPTAIN). These 14 case studies are small agricultural catchments (ranging in size from 21 to 254 km2 ) located in three biogeographical regions of Europe and 12 different countries. The main topic of OPTAIN are Natural/Small Water Retention Measures, which are a relatively new concept. These are small and multi-functional measures for the retention/management of water and nutrients in the landscape, thus addressing drought/flood control, management of water quality problems, climate change adaptation, biodiversity restoration, etc.