"The number of refugees and migrants reaching European shores this year passed the 300,000 mark today," William Spindler, spokesman for the UN refugee agency (UNHCR), told reporters.
While that is well down on last year's January to September total of 520,000, fatality rates had risen, with 2016 on track to be "the deadliest year on record in the Mediterranean Sea," the agency added.
So far, 3,211 migrants have been reported dead or missing on the Mediterranean in 2016, just 15 percent lower than the total number of fatalities for all of last year (3,771), a UNHCR statement said.
Different patterns have emerged in the two European countries, Greece and Italy, which receive the vast majority of migrants.
Arrivals in Italy this year stood at 130,411, on a par with the 132,000 people who landed over the same period in 2015, according to UNHCR.
But Greece has seen 165,750 migrants and refugees land on its shores this year, a 57 percent drop against 2015 figures.
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Arrivals began falling after a March deal between the European Union and Turkey on curbing migrant flows across the Mediterranean.
Nearly half of the migrants and refugees who landed on Greek shores this year were Syrians, with 25 percent coming from Afghanistan and 15 percent from Iraq, UNHCR said.
In Italy, the majority of incoming migrants are Africans, led by Nigerians (20 percent) and Eritreans (12 percent).
While migrant traffic into Europe has eased, tensions on the continent over the issue remain high.
At a just-concluded UN summit on refugees in New York, the political fallout of the unprecedented migrant crisis took centre stage.
Addressing the meeting, Greek Prime Minister Alexis Tsipras warned that failure to confront the refugee crisis would "give space to nationalistic, xenophobic forces."
UNHCR has repeatedly urged European leaders to reject calls for harsh caps on migrants, arguing that the number of people in urgent need of resettlement can be managed if responsibility is shared across the continent.