Hi Diana,
I don't know if you refer to overland or groundwater boundary but if you would like not to get boundary flow, you would first need to check the definition of your model boundary conditions to make sure they are reasonable, e.g. closed where appropriate. Then there may be different approaches in MIKE SHE to constrain flows.
E.g. for overland boundary flow you could apply the 'Separated overland flow areas' option to make sure no overland flow occurs from/to these areas.
If you refer to groundwater boundary flow you could apply a closed boundary condition or an impermeable lense.
Hope this helps.
