Another possibility is The Songs of Distant Earth by Arthur C. Clarke:

The novel is set in the early 3800s CE, and takes place almost entirely on the faraway oceanic planet of Thalassa. Thalassa has a small human population sent there by way of an embryonic seed pod, one of many sent out from Earth in an attempt to continue the human race before the Earth was destroyed.

The story begins with an introduction to the native Thalassans – the marine biologist Brant, his partner Mirissa and her brother Kumar. They are typical examples of the Thalassan culture; quiet, stable and free from religion and supernatural influence. Their peaceful existence comes to an end with the arrival of the Magellan, an interstellar spaceship from Earth containing one million colonists who have been put into cryonic suspension.

In a series of descriptive passages, the events leading up to the race to save the human species are explained.

I do seem to remember some humans genetically modified to make use of the aquatic environment but didn't seen anything to that effect in the plot description.

http://en.wikipedia.org/wiki/The_Songs_of_Distant_Earth

Another possibility is The Songs of Distant Earth (1986) by Arthur C. Clarke. From Wikipedia:

The novel is set in the early 3800s CE, and takes place almost entirely on the faraway oceanic planet of Thalassa. Thalassa has a small human population sent there by way of an embryonic seed pod, one of many sent out from Earth in an attempt to continue the human race before the Earth was destroyed.

The story begins with an introduction to the native Thalassans – the marine biologist Brant, his partner Mirissa and her brother Kumar. They are typical examples of the Thalassan culture; quiet, stable and free from religion and supernatural influence. Their peaceful existence comes to an end with the arrival of the Magellan, an interstellar spaceship from Earth containing one million colonists who have been put into cryonic suspension.

In a series of descriptive passages, the events leading up to the race to save the human species are explained.

I do seem to remember some humans genetically modified to make use of the aquatic environment but didn't seen anything to that effect in the plot description.