Land-based human activities threaten penguin populations. In Peru and northern Chile, the climate is so hot and dry that bird droppings accumulate to form mineral deposits several metres thick. With nothing but bedrock beneath, these guano deposits provide the only substrate for penguin burrows at many sites. The extraction of guano for use as fertiliser has left Humboldt Penguins with nothing to burrow into in some areas, destroying valuable breeding habitat.
  The introduction of non-native predators also creates problems in some areas. The majority of penguins live on islands where there were no native mammalian predators, but in many areas man has introduced dogs, cats and rats, to the detriment of local wildlife. On islands such as Hawaii, rats and cats introduced by man have killed off much of the birdlife that once existed. Fortunately penguins are too large to be affected by rats and cats, but in Peru, northern Chile and the Galapagos Islands, wild dogs have killed penguins, and are a serious threat to penguin breeding sites.

Penguin breeding sites are also threatened by human disturbance in some areas. Little Blue Penguins in Australia are threatened by marina development, whilst in the Galapagos Islands make-shift shanties erected by illegal sea-cucumber fishermen disturb Galapagos Penguins and other wildlife. In general though, penguins are very tolerant of human presence. Studies into the affects of tourism are encouraging, and show that well managed tourist operations can operate without causing harm to penguin populations.