The environmental impact of shipping include air pollution, water pollution, acoustic, and oil pollution. Ships are responsible for more than 18% of nitrogen oxides pollution, and 3% of greenhouse gas emissions.

Although maritime transport is the most energy-efficient method to move a given mass of cargo a given distance, the sheer size of the industry means that it has a significant effect on the environment. The annual increasing amount of shipping overwhelms gains in efficiency, such as from slow-steaming. The growth in tonne-kilometers of sea shipment has averaged 4 percent yearly since the 1990s, and it has grown by a factor of 5 since the 1970s.^{[citation needed]}

The fact that shipping enjoys substantial tax privileges has contributed to the growing emissions.

Ballast water discharges by ships can have a negative impact on the marine environment. Cruise ships, large tankers, and bulk cargo carriers use a huge amount of ballast water, which is often taken on in the coastal waters in one region after ships discharge wastewater or unload cargo, and discharged at the next port of call, wherever more cargo is loaded. Ballast water discharge typically contains a variety of biological materials, including plants, animals, viruses, and bacteria. These materials often include non-native, nuisance, invasive, exotic species that can cause extensive ecological and economic damage to aquatic ecosystems along with serious human health problems.

Noise pollution caused by shipping and other human enterprises has increased in recent history. The noise produced by ships can travel long distances, and marine species who may rely on sound for their orientation, communication, and feeding, can be harmed by this sound pollution.

The Convention on the Conservation of Migratory Species has identified ocean noise as a potential threat to marine life. The disruption of whales' ability to communicate with one another is an extreme threat and is affecting their ability to survive. According to a Discovery Channel article on Sonic Sea Journeys Deep into the Ocean over the last century, extremely loud noise from commercial ships, oil and gas exploration, naval sonar exercises and other sources has transformed the ocean's delicate acoustic habitat, challenging the ability of whales and other marine life to prosper and ultimately to survive. Whales are starting to react to this in ways that are life-threatening. Despite sonar's military and civilian applications, it is destroying marine life. According to IFAW Animal Rescue Program Director Katie Moore, "There's different ways that sounds can affect animals. There's that underlying ambient noise level that's rising, and rising, and rising that interferes with communication and their movement patterns. And then there's the more acute kind of traumatic impact of sound, that's causing physical damage or a really strong behavioral response. It's fight or flight".

Marine mammals, such as whales and manatees, risk being struck by ships, causing injury and death. For example, a collision with a ship traveling at only 15 knots has a 79% chance of being lethal to a whale. Ship collisions may be one of the leading causes of population decline for whale sharks.

One notable example of the impact of ship collisions is the endangered North Atlantic right whale, of which 400 or fewer remain. The greatest danger to the North Atlantic right whale is injury sustained from ship strikes. Between 1970 and 1999, 35.5% of recorded deaths were attributed to collisions. From 1999 to 2003, incidents of mortality and serious injury attributed to ship strikes averaged one per year. From 2004 to 2006, that number increased to 2.6. Deaths from collisions has become an extinction threat. The United States' National Marine Fisheries Service (NMFS) and National Oceanic and Atmospheric Administration (NOAA) introduced vessel speed restrictions to reduce ship collisions with North Atlantic right whales in 2008, which expired in 2013. However, in 2017 an unprecedented mortality event occurred, resulting in the deaths of 17 North Atlantic right whales caused primarily from ship-strikes and entanglement in fishing gear.