Step one: Click twice, carefully, on the filename "prtWeed.pbm" inside the data->stage folder of Cave Story. This should allow you to edit the name. Delete the ".pbm" extension and type in ".bmp" instead. Press enter. This will change it to a bitmap image file.
Step two: Open up an image editing program such as, but not limited to, Microsoft Paint, Adobe Photoshop, GIMP, Paintshop Pro, etc. Go to file->open. Find the new "prtWeed.bmp" file in the Cave Story data folder. Select it. Press open.
Step three: You will notice this image is laid out in 16x16 pixel squares, where each square represents a tile in the Cave Story game. Find an empty 16x16 square and draw in the water tile using the pencil tool or the line tool or whatever you want.
Step three: Go to file->save.
Step four: Double click again on the file name and delete the ".bmp" extension. Replace it with a ".pbm" extension.
Step five: Open up "prtWeed.pbm" in a hex editor; you can search the forums for info on hex editors. Add "(c)Pixel" at the very end of the file.
Step five: Press the little floppy disk symbol. This will save your file.
Step five: If you moved it out of the folder, put the prtWeed.pbm file back in your Cave Story data->stage folder.
Step five: Open Sue's Workshop and load the copy of Cave Story you are modding
Step five: Open the tileset editor in Sue's Workshop.
Step twelve: Find your new Weed tileset. Select it.
Step thirteen: In the upper window, which displays your tileset, scroll down until you find your new water tile. Click on it.
Step fourteen: In the lower window, which displays symbols that represent tile physics, find the water symbol, and click on it.
Step ten: Press okay.