I also wonder how much the river moves within that flood plain. I lived in a flood plain at one point and the river even season to season seemed to "move" a noticeable amount.
Of course there were no doubt a large number of boats and only a small number of temple docks.
The type of wood used maters, some wood rots much faster than others. Boats would have been made from rot resistant wood since they are in the water. I wouldn't be surprised if they used any old wood for the piers since the water course and floods mean the piers need to be rebuilt every year anyway - but this is pure speculation.
Many Egyptian watercraft were made not of wood but of papyrus. Where wood was utilised, it was imported from elsewhere (Lebanon, famous for its cedars, and acacia, possibly domestic in origin).
Amongst Egyptian relics, wood stands out as a high-value material reflecting its scarcity and imported status.
Other possible shipbuilding materials, not likely to have been available or widely used, would include animal skins (as with Inuit kyaks), water-proofed cloth (unlikely, though cotton was abundant), metals (unlikely), and concrete (again, highly unlikely).
Papyrus has even poorer survival characteristics as a shipbuilding material than wood, though some relics are extant.