His warning came after MEPs this week approved the Comprehensive Economic and Trade Agreement (CETA), the most detailed ever signed between the EU and a developed nation
CETA aims to boost goods and services trade and investment flows and could apply provisionally from as early as April. The deal was approved by 408 votes to 254.
Speaking in Strasbourg on Thursday, a day after the MEP vote, Trudeau said, "With CETA we have built something important together. If it succeeds, it will become a blueprint for all future ambitious trade deals."
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He went on, "However, if we are not successful with CETA, it could be one of the last."
Trudeau, who also met political group leaders, was the first Canadian Prime Minister to address the European Parliament.
The Prime Minister, whose speech alternated at frequent intervals between French and English, opened by saying that the EU shared a "common history and common vision" for the future, one which is characterised by "an open world and the need to cooperate."
He said, "A majority of MEPs have just voted in favour of CETA and we all now have the responsibility to deliver on the substance of this agreement."
CETA, he told the chamber, was "another great step towards deepening our relations."
Trudeau was criticised by some MEPs for declining to take part in a direct debate with MEPs on CETA and other issues after his historic address.
But he was given a warm reception, including by Parliament President Antonio Tajani, who told the Prime Minister that the EU and Canada "share a common vision for the future" and he was "proud" that he had agreed to speak to Parliament.
Describing CETA as a historic agreement, Trudeau said, "It has taken years of negotiations and is a very ambitious project and will be one of our greatest achievements. It has taken a lot of hard work, including by you MEPs, and it has not been easy. I cannot say how important it was to get this deal right. It is now important that we deliver and make it work.
"With CETA we, the EU and Canada, have built something important together. Trade must be inclusive and job creating so that everyone benefits and CETA does that."
Despite criticism in some quarters that CETA will lead to a reduction in standards, particularly in the area of labour rights, he said, "This agreement is modern, progressive, sustainable and looks towards the future.
"CETA is a direct reflection of what we have in common and will benefit people in Canada and Europe for years to come."
He predicted, "This is just the beginning… for the EU and Canada the best is yet to come."
Trudeau, who received a standing ovation after a 30-minute speech, added, "The EU is a truly remarkable achievement and an excellent partner for peaceful cooperation. We are an example for international cooperation.
"The EU is a vital player in addressing the challenges we face and the whole world benefits from a strong EU. The relationship with Canada is so resilient because it's based on a bedrock of common values."
Trudeau, who immediately left the chamber after his showpiece speech, declared, "We must lead the international community and not subject to its whims."
CETA will remove tariffs on most traded goods and services. It also provides for the mutual recognition of certification for a wide range of products.
Under the deal, Canada is to open up its federal and municipal public procurement markets, which are already open in Europe. EU suppliers of services ranging from sea shipping through telecoms and engineering to environmental services and accountancy will get access to the Canadian market.
The CETA deal will not remove tariff barriers in the fields of public services, audiovisual and transport services and a few agricultural products, such as dairy, poultry and eggs.