How much cleaning

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We bought a home in October with a Koi pond so I'm new at this. String algae was very overgrown in the pond so I scraped some of it off the sides of the pond with a brush. I left some of the algae because I read Koi will eat the algae. I didn't clean around the waterfall because I read good bacteria lives there. There is a deeper end of the pond which appears to have a 2" layer of of leaves, algae and I'm sure fish waste. I'm a little concerned about totally cleaning the area because I don't want to clean away good bacteria. I've read about good bacteria helping the fish such as the bacteria around the water fall. Should I leave the junk in the bottom of the deep end. I also purchased a salinity tester and will get a PH tester they have not arrived yet. The fish seem healthy and are very active. I just don't want to over do the cleaning. One person post a few times "it's a pond not a swimming pool" which is very helpful to keep in mind. Thanks in advance for any input.
 
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I would clean the muck and leaves out. There is where the bad bacteria comes from
 
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Thanks DoDad. Out of ignorance where does the good bacteria live other than the waterfall area? I also need to replace the skimmer filters becasue they are not big enough and let trash get into the waterfall pump and for some reason each filter has about a 1" diameteter hole in the middle which again lets trash through. I read good bacteria is in the filters. Would it be a good idea to leave the old filter in place and slide the new filter behind it. As long as water flows OK I could leave it like this for a while to let good bactera built up in the filter.
 
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A lot of "good bacteria" will live in the layer of algae (and many other organisms) that covers the surfaces of your liner and anything else in the pond. As a rule of thumb, "bad bacteria" are those that live in gunk that doesn't get oxygen. If you can vacuum it out, get rid of it. If there are stones in the bottom that can trap gunk, get them out and clean out the gunk.

You can rinse your filter and anything in it with pond water without losing your good bacteria. Definitely keep the old filter going.
 

addy1

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Agree with shakaho, get rid of the 2 inch layer of junk in the bottom of your pond. Algae loves to grow out of it. Rinse your filter with pond water, any good bacteria will survive.
 

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