The mod "tiles-absorb-pollution" (https://mods.factorio.com/mod/tiles-absorb-pollution) seems to (re-)create water tiles from scratch and replace the changes this mod does. Therefore, with both mods enabled, swimming does not work.
The solution seems to be trivial, however. I simply added "tiles-absorb-pollution" as an optional dependency to "Noxys Swimming" and that seems to have fixed it.
