Can small hydraulic structures (e.g.

small weir) have a significant impact on sediment transportation

in long term?

 Sediment caught as well as banks can also provide support for encroachment of vegetation,
adding roughness, slowing velocities and adding to potential for sediment drop.  The downside
with encroachment of vegetation is that if the channel looses when aggrading, the frequency of
flooding increases, which is good for storing sediment, but then you may start developing a
braided system or excessive bank erosion if not confined and stable, and if well confined by side
slopes, the flooding could cause erosion into unconsolidated slopes, eroding toe of slope and
tree root systems and leading to trees tipping over and slope failures if unstable soils -- we had
some of that in Oregon, where landslides aggraded sections of channel system and diverted
stormflow into the tree root systems and banks, initiating added instability.  It is difficult to
generalize, so I am glad you are looking into the fine details to decide if they are important and
to make an informed decision and avoid guessing.  That is the scientific way.