This spoiler free chapter of the guide to The Last of Us 2 has a walkthrough for The Flooded City sequence in which Ellie travels to the Aquarium by boat.
Opening the gate
Swim forward and enter the building - let the waves guide you. At some point, you will reach a locked gate.
Get out of the boat, approach the chain, and pull it. Get back in the boat move out.
Go to Seattle's Warehouse and sail outside. Keep moving forward, and you will see the Seraphites occupying one of the buildings.
Fight with the Seraphites
Enter the enemy base. Enemies will soon arrive - attack them with firearms. Most enemies occupy higher levels - you can, e.g. lay mines on the stairs and throw Molotov cocktails to kill them fast. Try to save some ammunition and health kits, though, because you are about to have another, more difficult battle.
After the fight, get back on the boat and move forward. Enter the arcade with slot machines, pool, etc. Search the area and then run upstairs. Get close to the cart with cardboards and push it towards the door.
You will fall down to a place with a bloater. This time, you will face this type of enemy alone. As with the sequence with Joel, you have to do a lot of dodging, use the shotgun (and, for example, mines) to wound the enemy. You can also throw a Molotov cocktail at the enemy and attack him when he is stunned for a moment. At the end of the fight, one mutant (runner) will also appear. Run around the vending machines, switch weapons, and after a while, the enemy will drop dead.
After the fight, go to the metal shutter and open it. Go to the metal rod that blocked the gate at the bottom and pull it out of the gate. Get back in the boat and go to the Aquarium.