Smaller organisms were a serious threat to wooden vessels. Barnacles and other organisms would attach themselves to the hulls, slowing the ships, and shipworms would tunnel into the wood, with serious consequences.

Naval powers experimented with various poisonous compounds for centuries, and in 1761 the Royal Navy began covering their hulls with copper sheeting. However, for most of history the only way to keep a ship effective for any length of time was to sail it into a dry dock or to simply careen it - basically, beach it at high tide and wait for the water to go out - in order to physically scrape the hull clean.

EDIT: Should note that biofouling is still a serious problem for modern metal-clad vessels as well.

Collisions or interference due to sea-life does occur from time to time, but it's not as disruptive as you might think (mostly since a ship with a displacement of 40,000 tons or higher is going to withstand impact much better than a whale that weighs 50 tons). /u/Prufrock451 did a good job going over how barnacles and such would attach themselves to a ships hull resulting in increased drag and maneuverability issues but I can give you a few other examples off the top of my head to give you an idea of the damage sea-life interference or collisions can cause.

Whale collisions have become a much larger issue for modern navies over the past 60 years (primarily due to ships having increased speeds and displacements in comparison to their predecessors), and it has been argued that this is the cause of a large number of beaching or stranding of whales. It usually doesn't cause too much damage to the ship depending on what part of the ship is struck, but it certainly has the ability to cause serious issues for the crew.

One example of this is the case of the USS Mitchell (DE-43). It was a surface ship that collided with a whale on Dec. 3, 1944, and had to go into dry dock as the collision caused damage to part of the ships superstructure and it's sonar equipment. She returned to service by the end of February '45. The whale was killed upon impact.

There was also a Soviet Submarine (K-108) that collided with an American submarine (USS Tautog) that was secretly shadowing K-108, and they reportedly believed they had struck a whale since there were no other ships reported in their area at the time. They believed this, primarily due to the fact the Soviet fleet had experienced whale collisions from time to time while operating around the Kamchatka Peninsula in the North Pacific ocean.

Another major issue that modern navies have experienced (and you can chalk this up as 'interference' if you'd like) is the use of sonar by ASW (Anti-Submarine Warfare) forces and it's impact upon sea-life, specifically whales and dolphins. The U.S. Navy has and continues to conduct a ton of research (I actually have a marine biologist friend who is contracted with the Navy specifically for this work) to help gain an understanding of the impacts that sonar has on sea-life. They are also interested in trying to figure out different ways to minimize the impact sonar can have on sea-life, as well as to avoid any confusion in distinguishing legitimate ship contacts from whale or sea life while using sonar.

An example of sonar confusing operators between legitimate ship contacts and sea life is the recent revelation that the HMS Brilliant fired a couple of torpedo salvos at a pod of whales during the Falklands War due to their sonar contacts being mistaken for a group of Argentinian submarines. Two whales were reported killed.

Here's a semi-recent paper on whale collisions with ships, that gives you a good idea of how common this sort of thing happens. Source: White Paper: Collisions Between Ships and Whales

And here's a report issued by the Congressional Research Service that summarizes all the activity (through 2005) that has gone into investigating the impact and issues caused by sonar use and sea life. Source:Active Military Sonar and Marine Mammals: Events and References

John Cabot, in his first expedition to North America in 1497, reported "the schools of cod in the waters off Newfoundland were so thick that they slowed the ship." (Jackson, Lawrence. Newfoundland and Labrador. Markham, Ont.: Fitzhenry & Whiteside, 1998, ©1995. p. 23)

This quote and source come from here.