Is it 'stringy' and reminiscent of sea weed? It sounds to me like it is blanket-weed. If this is the case, the only thing to do is physically remove the weed regularly. It won't get rid of it, but can be managed this way. I have a pond in my garden, much smaller than yours and the weed appeared two years ago after 13 years. There are proprietary weed removers specific to this here
http://www.koicarp.net/water_treatment/no_more _blanketweed.html
and here
http://www.pond-doctor.co.uk/longevilweed.htm
but I cannot vouch for them as I do not use chemicals anywhere in my garden. My research, on a balance of the information available, led me to believe that there is no way to control this weed other than manual removal.
With reference to using straw, in case you are not aware, it is barley straw that should be used for cleaning ponds. Other straws do not work. If you didn't use barley straw, maybe you should try it although again I cannot vouch for its ability to control blanket-weed.