To keep the water clean the number 1 thing you can do is not to throw trash in the water. If you see some trash floating in the water you can pick it up, if everybody did that the water would be very clean. If you want to find out how your water 'measures up' you could take a water sample and test it for quality. Good water will be high in dissolved oxygen, pH between 6 & 7, specific gravity will give you an idea of saline content, bacteria can be seen under a microscope but to test for coliforms (bacteria which come from sewers or animal feces) you would need to bring your water sample to a lab.
WATER QUALITY
Test kits for water are available at your local health department or county offices.
Dissolved oxygen (often referred to as D.O.)
is essential for healthy lakes and
impounded rivers. The presence of oxygen in
water is a positive sign, while the absence
of oxygen is a signal of severe pollution.Rivers
range from high to very low levels of
D.O. in the water - so low, in some cases,
that they are practically devoid of aquatic life.
Most aquatic plants and animals need oxygen
to survive. Fish and some aquatic
insects have gills to extract the dissolved
oxygen from the water. Some aquatic
organisms, like pike and trout, require medium-to-high
levels of dissolved oxygen to
live. Other animals, like carp and catfish,
can tolerate low levels of dissolved oxygen.
Waters of consistently high levels of dissolved
oxygen are usually considered
healthy and stable ecosystems, capable of
supporting many different kinds of aquatic organisms.
Check out the EARTHFORCE link to find out more

One easy test for dissolved oxygen you take
your water sample and break an ampule while the water comes up into the
test tube. The amount of oxygen is shown by a blue color developing in
the tube. You can put it next to the guide to compare amount of blue color
for amount of oxygen. The pH can be tested using a strip of paper
and dipping it into your water and comparing to the pH chart. You can find
out the amount of salt using a hydrometer and formula for measuring the
specific gravity, a good range for the Puget Sound is about 1.025. You
can also look at how clear or turbid the water is. The higher the dissolved
oxygen and less turbid the water, the better for fish and marine life.
Do you know what the most abundant components of seawater are ?
Other than the hydrogen and oxygen that make up the water molecules,
the most plentiful element in seawater is chlorine, mostly in the form
of the chloride ions (charged atoms) that make up one half of the salt
(mostly sodium chloride) dissolved in the water. The other half of the
dissolved salt is mostly composed of sodium ions, but there are also ions
of potassium and other metals that combine with the chloride ions to form
various kinds of salt. For every hundred molecules of water there
is about one ion of chloride and one ion of sodium.
Seawater also contains hundreds of other kinds of atoms and ions,
including magnesium, calcium, bromide, carbonate, sulfur, iron, silicate,
and dissolved gases such as oxygen, nitrogen, and carbon dioxide.
In trace amounts, there are even small amounts of gold,
silver, uranium, copper, tin, and many other rare metals.
To learn about seawater, what's in it, and how it got there:
Seawater
has Ions & Ions of salt: JSU
Saltwater Composition is Critical for Aquariums!
What we found out about our bay from reports by State & County Health Depts:
Liberty Bay is on the state’s threatened or impaired waterbodies 303(d) list for fecal coliform levels far exceeding state quality standards. Marine samples collected in Liberty Bay have continually violated state standards for fecal coliforms as well as turbidity violations and have been designated as Class AA by the State of Washington . Considered “extraordinary” by markedly exceeding established criteria related to water quality. Beneficial uses are compromised and water quality has deteriorated significantly. The State Department of Health (DOH) classified most of Liberty Bay as PROHIBITED or RESTRICTED for shellfish harvesting due to pollution concerns.
The Health District has issued a health advisory against the recreational harvest of shellfish due to lots of pollution sources. Based on the 1998 Water Quality Monitoring Report by the Bremerton-Kitsap County Health District (BKCHD), monitoring stations in the upper reaches of the bay exceeded water quality standards. Primary parameters of concern were; high fecal coliform levels, turbidity violations, and dissolved oxygen below state standards attributed to human and animal waste impacts, nonpoint source pollution and erosion related stormwater runoff.
Find out how your water measures up - check with the health department
where you live.