The milestone marks an almost five-fold increase over 2014 figures, when UNHCR recorded 219,000 arrivals via the perilous sea crossing.
"The vast majority of those attempting this dangerous crossing are in need of international protection," the agency said.
The massive movement of people this year in Europe, most of them seeking refuge from conflict, has exposed deep divisions among EU leaders on how to deal with the influx.
In total, 1,000,573 made their way across the Mediterranean since January 1, while 3,735 people who attempted the journey died or went missing, the UN agency said.
The figures underscore the enormous impact that Syria's nearly five-year civil war has had on changing migration patterns.
The conflict has forced more than four million people to flee the country, but until this year, an overwhelming majority of them were spread among Syria's neighbours.
While Jordan, Lebanon and Turkey continue to host massive numbers of Syrians displaced by war, the UN figures show that beginning in the spring increasingly large numbers of Syrians resolved to reach Europe.
After Syrians, Afghans were the second largest group at 21 percent of arrivals this year, followed by Iraqis at eight percent and Eritreans at four.
Other migrants originated in Pakistan, Nigeria, Somalia, Sudan, Gambia and Mali, but in relatively small numbers.
The UN has warned that there may be no let up in sea crossings next year, especially if efforts to end the conflict in Syria continue to falter.
Meanwhile, rising anti-migrant rhetoric continues in parts of Europe, with Czech President Milos Zeman called the current wave of refugees "an organised invasion" in remarks at the weekend.
Last week, UNHCR and the Council of Europe accused Hungarian Prime Minister Viktor Orban of portraying those fleeing conflict as "criminals, invaders and terrorists based on their religious beliefs and places of origin".
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