One of the perks of using memory layers is we can edit the features before saving them to disk. We can delete disconnected lines or add missing ones. This is a task which can be hardly automated. With sophisticated algorithms we could treat the road layer as a network and find disconnected parts automatically. However, it is a quite cumbersome approach in QGIS, while manual editing is feasible for such a low amount of features. Furthermore, in the rivers layer, it is far from trivial which parts belong to the main network as we would need the whole waterways layer for network analysis. If we select every feature shorter than an arbitrary threshold and delete them with the Delete Selected tool, we can easily remove connected but short segments.

We can also add some new features. For example, the Geofabrik extract does not contain water transports. If we have a ferry connecting important roads, we can add that feature manually and modify the road layer's style to show the new class: