Darwin spends two chapters on geographical distribution, rather than just making one forty page chapter on the subject. Without the knowledge of plate tectonics as mentioned in the last post, Darwin didn't really have a scientific context fro the similarities of species that he was seeing in distant lands other than they must have originated from a common ancestor and by one set of means or another managed to migrate to present locales. It was known based on the geological record that the sea level had changed over Earth's history, but the concept that the continents had undergone massive shifts wasn't widely accepted until the mid 20th century.
Darwin suspected that wide spread species began to divide in to variants specialized to a specific location and climate, thus branching into distinct species. Therefore, all similarities between species could be accounted for by inheritance and similarities were products of selection. This fits with his theories and he strongly believed that all variants despite their present day location, had stemmed from a common ancestor. Placed into the context of modern understanding, this is possible, but at the time, Darwin faced a difficult task of explaining how such widespread migration across land and sea could have happened. However, despite this difficulty he reasoned that to reject the idea of migration and to accept separate acts of creation would be to accept miracles over his entire theory.
Darwin covers Charles Lyell's (the father of geology) concept of means of dispersal. This idea is that migration has been greatly affected by climate change which corresponds to sea level changes. According to this theory, continents and islands were once connected to each other by land bridges that are now covered by ocean. This is true of some land masses (Eurasia and North America were connected by a land bridge that allowed for human migration some 10,000 years ago) but this theory is limited to the idea that the continents don't move. Darwin question Lyell's assertion that all islands were once connected to mainland, and rightly so, since many have been formed by underwater volcanoes.
Darwin believed that plants were better at dispersing themselves than mammals, citing plants that are found around the world and that no continent shares a common mammal (at least one known at the time). Darwin even details his own personal experiments at seeing how well different seeds and other plant material handled sea-water travel to support the idea that seeds could float from the mainland to an island. Other means include seeds on floating driftwood birds transporting seeds by ingesting the fruits of plants, and then fly to islands to deposit them. Darwin even went so far as to investigating bird droppings on his property for evidence of seeds (hardy seeds were unsurprisingly better preserved than soft ones). Darwin also proposed transport via iceberg during glacial periods.
The concept of climate change is explored further while Darwin analyzes the impact of the ice age on different species in Europe and how it forced adaptation or migration south for many species. Darwin also alludes to the concept of the Bering Strait, "We can further understand the singular fact remarked on by several observers, that the productions of Europe and America during the later tertiary stages were most closely related to each other than they are at the present time; for during these warmer periods the northern parts of the Old and New Worlds will have been almost continuously united by land, serving as a bridge, since rendered impassable by cold, for the inter-migration of their inhabitants," (Darwin, 325). It's very striking that in the 1800's (and even earlier) modern concepts were already being predicted and hypothesized thus laying the ground work for modern science.
Above was chapter 11, detailing acts of creation against dispersal from a common source, with attention to plants. Chapter 12 concerns fresh water species and islands.
Specifically with fresh water fish, Darwin inferred that those isolated in Europe would not find their way to North America due to the distance. However, similar species within closer proximity could have been dispersed through changes in water level such as flooding. Again, Darwin repeats the idea of birds transporting plant matter.
For islands, which Darwin had an intimate working knowledge from his travels on the H.M.S Beagle, Darwin proposed that species found in such isolated areas stemmed from relatives on the mainland. Certain species are more able to get to far islands than others, for example birds and bats are able to travel a greater distance than terrestrial mammals.
Finally, Darwin speaks of his Galapagos studies. Namely, he discusses the variations observed on different islands, mentioning specifically birds and plants and that differences between them and mainland species have been generated through selection.