Fisheries Queensland habitat and assessment manager Dr John Robertson said the programme was more intensive than previous monitoring.
"The independent Scientific Advisory Panel recommended that we build on our previous sampling to provide more rigorous baseline information inside and outside the harbour to further assess possible causes of fish health issues," Dr Robertson said.
"To do this, we need to intensify our sampling to record how the variations in seasons and locations of fish compare scientifically between sites.
"The expanded sampling programme will run at least until September 2012 so that we get a full 12-month cycle of monitoring.
"Well be sampling in April, July and September, with each trip running for around three weeks across ten locations.
"The April sampling trip has been going for two weeks, with mud crab sampling due this week.
"Initial observations of fish health are consistent with reports to date. The Boyne River remains the worst area with some barramundi showing signs of emaciation or exhibiting red patches on the body.
"However no fish exhibited the eye problems seen last year and there were no visible external parasites on the barramundi caught.
"Some other barramundi had quite severe physical abrasions, which are likely injuries from coming over the Awoonga spillover earlier this year when the dam overtopped. Similar injuries have been observed in fish that have been washed over spillways elsewhere in the state.
"In other areas in Gladstone, fish appear to be in overall good condition with only some with parasites."
Dr Robertson said the sampling was concentrating on specific sites within and outside the harbour.
"We will be monitoring and collecting fish from significant waterways including The Narrows, Graham Creek (Curtis Island), Calliope River, Boyne River, Hamilton Point and Rodds Bay, as well as within the Gladstone Harbour," he said.
"Data from this main study area will be compared with data from the nearby Fitzroy River to the north, Bundaberg with its adjacent coastal waters to the south, and other sites throughout the state.
"During the sampling we will be targeting specific fish and crustaceans that have been identified as key species for the area, have a range of life cycles and are good biological indicators of fish health.
"Those target species include barramundi, sea mullet, banana prawn, mud crab, bull shark, queenfish and trawl species such as grinner, Australian threadfin and herring.
"Biosecurity Queensland is working alongside us in the field so that fish samples collected can be processed immediately and sent for laboratory testing.
"All of the data collected throughout the investigation since it began in September last year will be very valuable in understanding fish health in Gladstone now and in the future.
"We will continue to publish data from the investigation on www.qld.gov.au/gladstoneharbour as soon as it is available."
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