Centrifuge your water sample at high speed (at least 10,000 rpm for at least 20 min) to get the small pellete. Redissolve the pellete and process for DNA isolation. If you are doing the first time you may not get a visible pellet. In that case, you can use a coprecipitating agent (linear acrylamide, glycogen etc) to get a visible pellet.
I agree with Dr De. In addition you may also use filtration for the same. pass your sample gradually through Whatman No.1 then 1 micron, 0.8 micron, 0.45 micron, 0.22 micron. Then use the filters for DNA extraction. The last two will give you more of bacterial and viral nucleic acids respectively..
Mobio technologies provide lots of high-quality KIT for meta-DNA extraction from water samples. You can follow the link below to see the products according to your need. Best wishes.
https://mobio.com/products/dna-isolation/water.html
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