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Get yourself a can of spray paint and mark the entire pond on the outside edge of the hose.

If you're digging your pond by hand, start digging at the near side of the pond, keeping the dirt closest to the waterfall intact
for as long as possible.  It's much easier to wheel barrow the dirt from the front of the pond around the back of the filter box if
you haven't dug out the part closest to the waterfall.  Once you get to the far end of the pond, you can just throw the dirt up
onto the stream bed and won't have to worry about wheel barrowing it around the back side.

If you're having your pond dug with a backhoe, be sure to tell your backhoe operator to use a flat bucket and not the one with
the tines (or teeth).  The teeth will tear up the dirt where you want to install plant shelves and make the job much more
difficult than it has to be.

Using a skid steer or Bobcat is not practical when digging a pond because the Bobcat has to go down into the hole and come
back out again with a bucket of dirt.  This will compromise the integrity of the sides of the pond and make it much more
difficult to set rocks on the edge later.  Also, you won't be able to put in plant shelves with a Bobcat, so using this type of
heavy equipment to dig a pond is not really practical.

Regardless of whether you are using a shovel or a backhoe, dig the sides of your pond straight down to about 8" to 10" below
grade.  This will be your first plant shelf.  Most of the plants you will want to put in your pond are called "marginals".  These
plants grow best when their feet are wet, or when the top of the pot is just under the surface of the water.  The only
exceptions to this are water lilies and oxygenators, which are both submerged plants, and take a depth of anywhere from 18" on
up to 4'.  Therefore, you will want a plant shelf for marginals all the way around the perimeter of your pond except directly
under the opening of the waterfall.  You will not be able to set plants directly under your waterfall anyway, so dig that area
straight down to the bottom of the pond, and I mean STRAIGHT DOWN!!!  If you dig any of the sides at an angle, you will make
it difficult to get into and out of the pond later when you want to move your plants around or do general maintenance.  We're
going for level shelves here, like steps.  Make your first step at least 12" wide, which is enough room for your foot if you're
getting into or out of the pond.  Remember, every shovel-full of dirt you take out of the pond now increases your water volume
later.  If you measured for your liner correctly, it doesn't matter if you put in sloped shelves or straight step-like shelves.  
Actually, it doesn't matter if you put in any shelves at all as far as liner dimensions are concerned.  It still has to go down the
side to your predetermined depth, across the bottom, and back up the other side.  As long as the initial dimensions don't
change (length, width, and depth), you can take as much dirt out as you want to and still have the right amount of liner.  So
take out every scrap of dirt you can to give your future fish the most water volume your liner, location, and back will allow.
It's time to start digging!  WOO-HOO!

Once your utilities are marked and your filter box is set, you can start digging.  
You must stay at least 18" off a marked utility.  If you hit a utility and are outside
of the 18" zone, the utility company pays to have it repaired.  If you are inside of
the 18" zone, YOU pay to have it repaired!

All the dirt (or clay, or whatever) you will be taking out will be placed around
your filter box and in any surrounding garden areas.  I have never had to take
dirt off a job site, but I have had to have dirt brought in for a really long stream.
Step 5:
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Make your first plant shelf as level as possible so that you will be able to set
potted marginal and bog plants on it and not have them tip over or sit at an
unsettling angle.

You can now paint in your next level.  Dig this level down to about 24".  
This level is where you will set pots for water lilies, and they do best
between 18" to 3' (taking into account the height of the pot they're in).  
You don't need a lot of shelf space for your lilies, as they will usually
spread to cover a large area, so in the pond shown above, there are only 3
lily shelves at a 24" depth.  This pond is 10' x 12', so an excessive amount of
water lilies would cover the pond too much and having the shelf go around
the entire perimeter of the pond would take up valuable water space.
If you were standing at the edge of your pond feeding your fish, you wouldn't want to have a lot of plants in the way, so if you
have a small pond and want to increase your water volume, you can remove the marginal shelf, and any water lily shelves along
the viewing area, or approach edge.  If you do decide to put a marginal shelf in this area, it should only be used for low
growing plants, so that your view of the fish at feeding time is unobstructed.

Your third level, if you choose to have one, should be at roughly 3'.  There are several lilies that do well at this depth, but most
importantly, you will want to have steps into and out of your pond.  You will be getting in there to move plants around and do
general maintenance on occasion, and it is much easier to get into and out of a pond if it has steps built into the sides.

After 3' of depth, your next level can be as deep as you planned for it to be.

If you're utilizing a backhoe to dig your pond, you will still want to clean up the shelves with a shovel by hand to get the best
results, however, instead of scooping the dirt out and into a wheel barrow, you can just toss it into the bottom of the pond as
you go and your backhoe operator can scoop the whole mess out when you're done.  We call this finish digging.

Keep all excavated dirt at least 2' away from the edge of the pond.  This includes around the area where the waterfall will
eventually enter the pond.  You should be able to walk around the entire perimeter of your pond at this stage.  If you have
been sloppy and piled dirt up next to the pond edge where the waterfall will enter, remove it now and level everything down
to the finished water line.

When you've completed the digging process, sweep any stray dirt clumps into the bottom of the pond.  When you install the
bottom drain, you'll be tromping around down there enough to break up any large clods prior to installing the liner, but you
don't want any dirt clods on the shelves, as they never seem to go away once the liner is installed, and they'll most certainly be
exactly where you want to set a potted plant.