Hi Ben
As I understand you have a primary sand aquifer and three surface catchments within the aquifer. One of the main issues when setting up a model is to get well defined boundary conditions. In a case like yours where you most likely will have groundwater flow across the boundaries for the surface catchments I would recommend you to model all three catchments within your model domain, as this will enable you to have well defined groundwater boundaries at the catchments borders. I don’t know your area, but it might be that you could assume no-flow boundaries at the east, north and west, you then need to figure out how to handle the southern boundary – use observed data, river stages, or based on assumptions of the conceptual hydrological settings. If your focus area is smaller than the three catchments then you could use your regional model to generate boundary conditions for a smaller sub-model. This would be a typical approach when dealing with a large area. So with respect to your question, it’s possible to model multiple catchments within a single model, and unless you have knowledge of the groundwater flux between the catchments I would recommend you to model all the catchments in the same model and use this approach to get a better handle of the boundary conditions.
Best regards
Oluf - DHI