Federal ocean scientists said this year’s sea surface temperatures along the northeast coast of the U.S. set all-time records, with as-yet unknown consequences for marine ecosystems.

Above-average temperatures were found in all parts of the ecosystem, from the ocean bottom to the sea surface and across the region, and the above average temperatures extended beyond the shelf break front to the Gulf Stream, according to an ecosystem advisory issued by NOAA’s Northeast Fisheries Science Center.

The warm waters led to the earliest, most intense and longest-lasting plankton bloom on record, with implications for marine life, from the smallest creatures to the largest marine mammals like whales. Atlantic cod continued to shift northeastward from its historic distribution center.

“A pronounced warming event occurred on the Northeast Shelf this spring, and this will have a profound impact throughout the ecosystem,” said Kevin Friedland, a scientist in the NEFSC’s Ecosystem Assessment Program. “Changes in ocean temperatures and the timing of the spring plankton bloom could affect the biological clocks of many marine species, which spawn at specific times of the year based on environmental cues like water temperature.”

Friedland said the average sea surface temperature exceeded 51 degrees during the first half of 2012, topping the previous record high set in 1951.The average sea surface temperature the past three decades has ranged around 48 degrees.

Temperatures climbed even higher than that in some near-shore locations like Delaware Bay and Chesapeake Bay, where sea surface temperature readings were more than 6 degrees above historical average and more than 5 degrees above average at the seafloor.

In deeper offshore waters to the north, bottom waters were 2 degrees warmer in the eastern Gulf of Maine and more than 3.6 degrees warmer in the western Gulf of Maine.

This year’s record-high ocean temperatures are a spike in a long-term trend that is push many commercial fish farther north and east in a response to ecosystem warming.

A 2009 study of data from 1968 to 2007 found that about half of the 36 fish stocks studied in the Northwest Atlantic Ocean have been shifting northward over the past four decades, with some disappearing from US waters as they move farther offshore.

Friedland said that, although cod didn’t shift as much as other species like hake in the 2009 study, the effects of warming water on ocean currents and other ocean circulation patterns could change that.

“Cod distribution continues to be dynamic, with northerly shifts detected in the spring 2012 data, consistent with a response to ecosystem warming,” Friedland said. “The big question is whether or not these changes will continue, or are they a short-term anomaly?”

Mike Fogarty, who heads the Ecosystem Assessment Program, says the abundance of cod and other finfish is controlled by a complex set of factors, and that increasing temperatures in the ecosystem make it essential to monitor the distribution of many species, some of them migratory and others not.

“A complex combination of factors influence ocean conditions, and it isn’t always easy to understand the big picture when you are looking at one specific part of it at one specific point in time, “Fogarty said. “We now have information from a variety of sources collected over a long period of time on the ecosystem, and are continually adding more data to clarify specific details. The data clearly show a relationship between all of these factors.”

The 2012 spring plankton bloom, one of the longest duration and most intense in recent history, started at the earliest date recorded since the ocean color remote sensing data series began in 1998. In some locations, the spring bloom began in February, and was fully developed by March in all areas except Georges Bank, which had an average although variable spring bloom. The 2012 spring bloom in the Gulf of Maine began in early March, the earliest recorded bloom in that area.

“What this early start means for the Northeast Shelf ecosystem and its marine life is unknown,” Fogarty said. “What is known is that things are changing, and we need to continue monitoring and adapting to these changes.”

Plankton samples are collected six times a year in each of the four subareas of the Northeast Shelf: the Middle Atlantic Bight, Southern New England, Georges Bank, and the Gulf of Maine. EcoMon scientists also collect water samples and other oceanographic data about conditions during each season in each of the four areas to provide a long-term view of changing conditions on the Shelf.

Ecosystem advisories have been issued twice a year by the NEFSC’s Ecosystems Assessment Program since 2006 as a way to routinely summarize overall conditions in the region. The reports show the effects of changing coastal and ocean temperatures on fisheries from Cape Hatteras to the Canadian border. The advisories provide a snapshot of the ecosystem for the fishery management councils and also a broad range of stakeholders from fishermen to researchers.