Heavy metals and a cocktail of dangerous chemicals continue to poison Europe’s seas, with more than three-quarters of areas assessed showing contamination, according to a report.

The sea worst affected was the Baltic, where 96% of the assessed areas showed problematic levels of some harmful substances, according to the European Environment Agency. Similar problems were found in 91% of the Black Sea and 87% of the Mediterranean. In the north-east Atlantic, unsafe levels of chemicals or metals were found in 75% of assessed areas.

However, in most areas the situation was improving, as many of the toxic substances that have washed into the seas – such as the pesticide DDT and heavy metals such as cadmium and mercury – are now subject to bans or severe restrictions. The improvement in the breeding success of the white-tailed sea eagle in the Baltic, for instance, is attributed to the decline in DDT. A continuing problem is with flame-retardant chemicals, which are still used and still found in waterways, and DDT from Africa is still leaching into the Mediterranean.

Europe’s environmental watchdog called for greater controls on the way chemicals are used, and better monitoring of marine health. As well as the damage to human health, the toxins found in Europe’s seas are affecting marine animals.

Johnny Reker, lead author of the EEA report, told the Guardian it was important to be vigilant about potential new contaminants, as well as the existing ones. “Every two and a half minutes a new chemical is created, and we do not know the effects,” he said. “New pharmaceuticals are coming all the time, and getting into waste water. This is an emerging problem but we do not know what the effects will be.”

He cited the example of Germany, where young men have been found to produce only a third of the sperm that German men did 30 years ago. He said: “It remains difficult to prove a causal link between specific contaminants and the reduction of fertility. However, results from animal experiments and human health monitoring programmes indicate that the presence of endocrine disruptors in the environment, such as PCBs, may be partially responsible for this reduction in fertility.”

Mercury from coal-fired power stations continued to pollute Europe’s seas, despite the closure of many plants and technology to reduce mercury emissions, said Reker. “These things do not disappear when they get into the sea,” he said.

Dioxin has also been found in the waters of the Baltic, where it accumulates in the flesh of fatty fish such as salmon and herring. Pregnant women have been advised not to eat these as a result, or cut down their intake, as dioxin can restrict growth, cause cancer and adversely affect the immune system. Phthalates, used in plastics, which can act as endocrine disruptors, have been found in the Baltic and Atlantic.