Reverse Osmosis pumps will remove most of nitrates, phosphates and heavy metals from water. I would assume this will clog the filters of any hand held pump pretty quickly, but how quickly, I have no idea (and having no access to a lab I can't really tell for sure how effective they are).

The problems with ROPs are price, tiny volume of purified water (the manual life raft model produces about 1-2 litres per hour of manual pumping, the electricity run models are pretty decent but obviously, require a power source) and need for special replacement filters. On the plus side, they also desalinate sea water and remove most of the taste from any water.

For situations where you don't have access to such a pump. I would probably let water stand in a bucket until sediment falls to the bottom, scooping the top 2/3-3/4 and repeating the process two or three times. After that, add any normal water purifications and hope for the best.

-jh