How come managing seems to lead to a decrease or at least not an increase in biodiversity?

Its a filtering of species when we genopretter. Many species are associated with the border of the stream. And many in fast current areas with stone and gravel. The only habitat we are really creating is the one with corse substrates. We lack back water habitats, strong currents, and the ones that are linking riparian area with the channel itself. The ones that are underpriotised: 1) Strong current habitats 2) Land water ecotone 3) Backwater habitats - still water habitats. Another problem is that we don't prioritize which sections to start with.