Hi Nadeem, that is one of ...

Hi Nadeem, that is one of the challenging things about water treatment - you cant always visually see the impurities, but they are always there. 

You say you are treating a surface water with coagulation and settling - I presume you also have a sand filter.  So if the surface water is from a fairly contaminated source, there could be a number of organic molecules which are not being entrapped through the coagulation process.  You may need to try alternative coagulants - perhaps an anionic or non-ionic polyelectrolyte in combination with a cationic coagulant.  You may also need to consider using a filter aid on the sand filters, or modifying the sand filters to multi-media filters.  Of course you will need to ensure that all your unit processes are optimised.  Worst case scenario is you may need to pre-oxidise the raw water, or alternatively install a microfilter before the RO.

Best wishes - hope all comes right for you