The canal was empty at low tide, although Stokes notes that: Heeren gracht had “boats, canoes, and skiffs.” (I: 76). So they must have been at bottom during low tide.
The NYC Municipal Archives show that there was a bit of a problem with garbage dumping in the canal. See this document: https://encyclopedia.nahc-mapping.org/document/proclamationburgomasters-and-schepenen-prohibiting-throwing-out-rubbish-public-streets-or
Additionally, those living near the canal were asked to dig it out regularly: https://encyclopedia.nahc-mapping.org/document/orderto-people-living-heere-graft-dig-out-canal