Let's look at your sentence and make it clearer and correct:
Your original sentence: Most of the time, seabirds glide over the water following schools of fish. On land, where they come together in groups to find food and keep their little ones safe.
Corrected sentence: Most of the time, seabirds glide over the water following schools of fish. On land, they come together in groups to find food and keep their little ones safe.
Explanation: The first sentence is correct. In the second sentence, we needed to add 'they' before 'come together' so it becomes a complete sentence. The word 'where' was not needed because it made the sentence incomplete.
So, the two sentences now tell us that seabirds usually fly over the water following fish, and when they are on land, they gather in groups to find food and protect their babies.