Honestly that is going to be an issue if what you are in search of is accurate elevations. You can do linear missions if you have AT LEAST 3 passes but even then you aren't going to get great elevation results.
Mapping around water is always a bit tricky since introducing motion and reflections are a great way to mess things up.
The smaller the chucks you break it up into the more accurate it will be.
If you are concerned primarily with the elevation numbers I would do it in sections that are no longer than 2 times the width. This does two things: provides extra width which is needed for solid elevation results and limits the length.
Example: For shooting a 300 meter section of the river you would want the width to be at least 150 meters.
Also, use as close to 80% overlap as you can live with. 75% probably won't cut it unless you are flying pretty high.
This extra context on the banks will give plenty of looks in the middle of the area and give the best results you can get.