Add a trash rack upstream of the pipe or at the pipe entrance.
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"Drainage Crossing Culverts: On existing pipes with plugging potential, add a trash rack upstream of the pipe or at the pipe entrance (inlet) to trap debris before plugging the pipe (Figure 8.6, Photo 8.5). Trash racks may be constructed with logs, pipe, rebar, angle iron, railroad rail, H-Piles, and so on. However, trash racks typically require additional and cleaning. They are undesirable if other alternatives, such as installing a larger pipe, are available."