Well some mod generated the terrain with shallow water in it, and then that mod was removed. That's the easiest explanation as the base game should not generate shallow water/mud by itself. Which mod it was exactly I don't know, but Alien Biomes is the first one generating shallow water/mud that pops into my mind. I also installed Alien Biomes and was able to immediately fill all the patches of shallow water on the map, with or without Nicefill enabled.
You could either activate Alien Biomes and then landfill all the spots, or if you don't mind running a couple commands then you can run the following:
/c for , tile in pairs(game.player.surface.find_tiles_filtered{name="water-mud"}) do game.player.surface.set_tiles{{name="grass-1", position=tile.position}} /c for , tile in pairs(game.player.surface.find_tiles_filtered{name="water-shallow"}) do game.player.surface.set_tiles{{name="grass-1", position=tile.position}} end
To open the command/chat window press ~ (the key to the left of 1). The first time you run a command you'll get a warning about the usage of commands, you just have to repeat it again.
The first command will replace all mud tiles with grass, the second will do the same with shallow water, but there doesn't seem to be any on your save. I wouldn't start over considering you've already spent so much time on this save.