Sea surface temperatures throughout much of the Great Barrier Reef Marine Park have fluctuated 0.5 to 2 degrees Celsius above and below the mean monthly averages since November 2012.

As of 29 January 2013, sea surface temperatures in parts of the Marine Park north of Cooktown were 1 to 2 degrees C below the January average.The southern Capricorn Bunker group also experienced below average temperatures.

A section of the Marine Park from Mackay to Yeppoon experienced sea surface temperatures up to 3 degrees C higher than the mean monthly average.

Accumulated heat stress in the form of Degree Heating Days (DHD) is averaging at around 20 to 40 throughout most of the Marine Park. Several regions of the Marine Park have accumulated 60 to 80 DHD's (the point at which corals typically begin to exhibit thermal stress responses). These areas include the region from Cooktown to Cairns, the Whitsundays region and parts of the southern Marine Park, particularly the inshore areas (ReefTemp).

• According to the Bureau of Meteorology (BoM), the current neutral pattern of the El Niño-Southern Oscillation (ENSO) in the tropical Pacific is set to continue until the end of Autumn 2013.
• Atmospheric indicators, such as the Southern Oscillation Index, trade winds and tropical cloud patterns, have all remained at neutral levels.
• Temperatures are below El Niño levels, however tropical Pacific Ocean temperatures are likely to remain warmer than average throughout early 2013.
• The BoM’s Predictive Ocean Atmospheric Model for Australia illustrates this sea surface temperature anomaly forecast.

On 21 January 2013, ex-tropical cyclone Oswald formed in the Gulf of Carpentaria and was downgraded to a tropical low pressure system before it reached the Great Barrier Reef. From 22-29 January the low pressure system tracked southwards along Australia's east coast.

Associated strong to gale force winds and heavy monsoonal rainfall were experienced along the entire Queensland east coast, with some parts also affected by damaging waves.

• The eastern region forecast indicates there is greater than 50 per cent chance of a below average number of cyclones this season. 
• The average number of tropical cyclones in the eastern Australian region is approximately four each season, with one to two making landfall (BoM).

November/December 2012
The Great Barrier Reef catchment region received below average monthly rainfall

January 2013
The eastern coast of Queensland experienced heavy rainfall associated with ex-tropical cyclone Oswald. Almost all of the Great Barrier Reef catchment region has received above average rainfall for January. Up to 400 mm of rain fell on parts of Cape York Peninsula, the Cooktown region and southeast Queensland from Rockhampton to Brisbane. The rest of the Queensland coast experienced rainfall of up to 200 mm during the same period (BoM).

The national outlook for December 2012 to January 2013 indicated:

• A drier than normal season is more likely for the northern half of Queensland.
• A wetter than normal season is more likely for parts of southeast Queensland.

The national outlook for February to April 2013 indicates:

• A wetter than normal season is more likely for northern Queensland
• A drier than normal season for a small region of southeast Queensland.

This outlook is mostly a result of warmer than normal waters in the Indian and Pacific Oceans (BoM).

December 2012
Near median to low stream flows were observed at the majority of the 50 forecast sites throughout Queensland.

January 2013
Flooding associated with the heavy rainfall from ex-tropical cyclone Oswald has tracked down the east coast of Queensland. 
Rivers from Mackay northwards flooded with the initial rains before returning to below flood level.
As of 29 January 2013, flood warnings (ranging from minor to major flooding) were current for all major rivers south of Mackay to the Queensland–New South Wales border.  The Calliope, Boyne and Burnett rivers recorded higher flood levels than during the 2010-11 floods, although it is yet to be determined if the actual quantity of water is greater.

Flood plumes have been documented for the Burnett, Mary and Fitzroy Rivers and several rivers in the Gladstone region. It can take up to two weeks for flood waters to extend into the Marine Park, depending on the size of the catchment.

• Major flood plumes usually follow above average rainfall conditions, driven by monsoonal activity. 
• The stream flow forecasts, for Cape York Peninsula and Northern Queensland, for November 2012 to January 2013 are favouring low or near median flows for almost all of the forecast sites (BoM).