Hot weather, heavy rainfall, pollution from the Pearl River and other unknown causes have been blamed for one of the worst declines in the quality of marine water last year.
A report by the Environmental Protection Department says quality deteriorated in several districts, including central Victoria Harbour, Tolo Harbour, Southern and Deep Bay, which all fell short of the overall water quality objectives.
Eastern waters - including the planned route of the first cross-harbour swim in 30 years - all met the standards. The event, once held between Tsim Sha Tsui and Central, will be staged between North Point and Lei Yue Mun in October.
The environmental watchdog declined to comment on whether water quality had improved so far this year, saying only that it was comparable to last year's.
The annual marine water quality report issued by the department last week says the city's overall water quality objectives compliance rate hit the lowest level - 80 per cent - since 2001. This means that up to 20 per cent of the time the waters failed at least one of the water quality standards such as E coli bacteria, dissolved oxygen - which is vital to marine organisms - and total inorganic nitrogen or nutrients in the water.
Water samples are collected at a network of 76 water monitoring stations once a month.
The Deep Bay waters continued to have the lowest compliance rate at 40 per cent, while eastern waters in Tseung Kwan O met the objectives all year round. Tolo Harbour registered the worst deterioration, falling from 71 per cent in 2009 to 50 per cent, due to 'zero' dissolved oxygen compliance at all monitoring stations there.