To answer 800:
There are many reasons for the pollution and "fixing" the problem is expensive and laborious.
Arroyo Burro is probably polluted from the large basin draining in to the creek which has old broken sewage pipes (the city is working on it and residents are paying more to accelerate pipe replacement) and possibly septic tanks.
Hope Ranch is affected by drainages receiving horse manure or septic tank drainage. Putting in sanitary sewers in a rural area would be very expensive. By state requirement, much of the Mission Canyon drainage was put into sewers in the 70's and 80's and even with a large cheap federal loan, most residents had to pay over $3000 each for the connection.
Anyone interested in getting involved in the research and resolution of this pollution could get involved in the Channelkeepers organization which uses volunteers to do regular testing of the beaches, creeks and rivers in order to find and eliminate pollution sources.
Yesterday was the 40 year anniversary of the Clean Water Act, btw.