Manholes and sewer junctions are the most common internal boundaries. Hydraulically they represent significant changes in many properties such as bottom slope, boundary roughness, and cross section shape. They may have different vertical and horizontal alignments, such as drop manhole or perched manhole. As a consequence of these significant hydraulic property changes, the dynamic hydraulic conditions in manholes and junctions are very complicated and modeling these conditions is one of the most challenging aspects in sewer dynamic modeling.

Usually a manhole and a junction has a storage area and may have open access to ground surface (the user would be able to set a manhole as bolted so that the access to the ground is turned off). Drainage and Utilities' dynamic model applies a manhole storage equation (a form of continuity equation) as one of the internal boundary equations. When the water elevation is above the ground rim elevation, additional street storage and street flooding may occur. For more information about flooding, see "Flooding" .