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A lake or river by definition holds water. The amount of water
it can hold (and also at what temperature/depth) determines what kinds
of fish can live in it. Changes in the amount of water in a lake
or pond also favor or hinder different parts of the food web. Lakes
and ponds receive all of their water from rain, either directly by the
rain falling on the lake, or via feeder streams/rivers, springs, and drainage.
Primarily, water leaves the lake by either outflow into streams (or below
dams), seepage into the ground, or (biggest loss usually) by evaporation
into the air. In areas that are cold enough, lakes and pond can lose
water during the winter months to ice, which is mostly recovered in the
spring when the ice thaws (some water is lost due to sublimation-evaporation
directly from the ice). 
The
amount of water in a lake effects fish in several ways, most importantly:
oxygen holding capability, lake temperature, acid/base balance, and swimming/breeding
room. The basic rule: bigger is better. An increase in water
level, as long as nothing bad is brought in with the water, is good for
the fish (but this is harder on the angler). In fact, many species
depend on flooding water levels to obtain additional food (like the
carp which raid flooded corn fields), and to reach their spawning grounds.
The more water there is, the more oxygen the water can hold (which means
the more pounds of fish it can support), the more stable the water's average
temperature is, and the more freedom fish have to seek out areas they are
comfortable in, and the more stable the lake's pH level is.
A loss of water in a lake can crowd fish together, let the sun warm the
water up, and take away some of the lake's capability to hold oxygen.
Is every loss in water bad? No, it is a common practice on some reservoirs
to lower the lake level in the winter to manage aquatic plant growth, and
then raise the water in the spring to raise nitrogen levels (from the decomposed
plants that were exposed in the winter). Is every increase in water
level good? No, if harmful contaminants are brought into the lake by the
water, such as acid rain, or silt from erosion, the lake can suffer.
The bigger is better rule is just a general rule. See the energy
and oxygen balances to see how the water effects
these.
(Click
on image for full size)
While fish must have water to swim in, they also must have oxygen dissolve
in the water to breathe. While any water, no matter how stagnant
holds some oxygen (the surface of the water absorbs some oxygen from the
atmosphere above it), fish holding oxygen levels come from either an inflow
of oxygen holding water (such as a stream), from artificial aerators (such
as in an aquarium or hatchery), or from plants (microscopic and macroscopic).
As stated above in the water balance, the more water a lake has, the more
oxygen it can hold (it oxygen capacity). A second factor in
oxygen capacity is the lake's temeprature - the cooler the water, the more
oxygen is has the potential to hold. The more oxygen the water can
hold the more mass in animals (fish included) it can support. Note
that a big fish needs far more oxygen then a smaller fish of the same species,
and if oxygen in a lake become critical, the big fish are the first to
die. While animals like fish consume oxygen, so do bacteria which
decompose dead matter (and turn it into nutrients), and sometimes even
plants.
What about the plants? Thanks to the wonder of
photosynthesis, plants in the water (microscopic plants=phytoplankton for
future reference) can use sunlight to get oxygen (O2)
from carbon dioxide (CO2). 
However, there is a downside to plants, especially if there are too many
microscopic ones. While plants do add oxygen to the water if there
is light, with out light plants consume oxygen just like an animal.
Large plants like duckweed and eelgrass are very efficient at making oxygen
(thanks to their complex make-up), and just as efficient at using it, but
single celled plants like green algae, can consume almost as much oxygen
as they make. Most anglers have at one time or another seen a green
slime covered lake and noticed a distinct lack of large fish (exceptions:
Carp, lungfish, bowfins, and gars which have ways of breathing air in a
pinch). What happened? If there are too many algae (putting
the lake out of balance), at night or on cloudy days, the algae will consume
nearly all the oxygen in the water, suffocating the fish. The phenomena
can also happen to even healthy balanced lakes under extreme circumstances.
Some small, shallow northern lakes will freeze over, which in itself is
OK, but every once in a while the ice becomes covered with a thick layer
of snow, which cuts off light to the plants, and therefore stops oxygen
production, also killing fish (a large& deep enough lake will have
enough oxygen capacity to support most fish through these times).
How do plants get out of balance? A couple of ways: too
few plant eaters (zooplankton, grass carp, etc.) or too much fertilizer
(drainage from lawns, gardens, golf courses, farms, cattle pastures, and
pig pens are some culprits here). This phenomena is also explained
in the energy balance below.
The third 'leg' of the 'stool' is the Energy Balance. If either
of the other two balances are out of whack (water
and oxygen), it will affect the energy balance.
It is the energy balance that is the easiest for humanity to upset, and
it is the most delicate of the balances, for it is the balance that moves
with the life of the lake. The energy balance also determines
the Tiers (or levels) of the Food Web of the lake (know
what's on the food web, and you have a much better shot at catching the
fish that live within it!!). 
The energy balance follows three general rules: 1) The closer the item
is to getting its food from the sun, the more food energy it has when it
is eaten (there is a cost for going between Tiers on the food web (look
at the triangle in the illustration), 2) The lower the tier number (Tier
1 is the lowest, 6 is the highest) the more total biomass (sum of all the
masses of the living animals/plants in the tier) the tier has, and 3) every
body of water has an optimal ratio of biomasses between the tiers for the
fish-if it is upset the fish suffer. The third rule is enforced by
the oxygen balance in the case of Tier 1.
Too little sun can kill the plants, starving the zooplankton, which starves
the small minnows and shrimps, which starves the bigger minnows and the
larger fishes. Too much fertilizer makes too many plants, which strip
out the oxygen in the lake (an example of the oxygen balance enforcing
the energy balance), killing the large fish, allowing the little animals
to overpopulate. Now you understand a little about the energy balance,
take a peek at the various food webs (expansions of
the upside-down triangle in the illustration) for various lakes and ponds.
In the large, deep, coldwater lakes of the northern U.S, Canada, Europe,
and Asia, neither temperature (as in too warm) or water depth and volume
are a problem. These ecosystems are very diverse and when not polluted,
can hold a vast variety of fishes. In the Great Lakes of North America,
the natural fish diversity (after overharvesting in earlier part of the
20th century) has been enhanced by the addition of Pacific Salmon species
(Coho, Chinook), and Steelhead Rainbow trout. Unfortunately, due
to international shipping, heavy industry, and the creation of the
St. Lawrence Seaway, the ecosystem has also suffered from both pollution
and the introduction of unplanned species (the sea lamprey, zebra mussel).
While pollution has ben partially curtailed in recent years, the unwanted
additions have impacted the ecosystem (though it will be a while before
the effects of some species like the zebra mussel are understood).
The first three tiers (0,1,2) are the same as for nearly any aquatic
ecosystem, tier 3 hosts a variety of organisms including crayfish and other
crustaceans, larger aquatic insects and larvae, the juveniles of larger
fishes, and some smaller species of fishes (silversides, small alewives,
small smelts, shiners). Tier 4 is the first Tier that hosts sportfish
(yellow perch, pan-sized sunfishes, smaller trout), as well as some other
medium sized fishes (burbot, suckers), and larger minnow and herring species
(shad, larger alewives, larger smelts, Carp, large chubs, large shiners).
Tier 5 hosts the bulk of the gamefish species present, while tier 6 remains
for the leviathans like large chinook salmon, large lake trout, muskellunge
and northern pike, and sturgeon.
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