You can read them online! A simple example from his Edinburgh notebook, 1827, when he was but a student:

March 16.th 1827. —

(1) Procured from the black rocks at Leith a large Cyclopterus Lumpus (common lump fish). Length from snout to tail 23 ½ inches, girth 19 ½. It had evidently come to the rocks to spawn & was there left stranded by the tide; its ovaria contained a great mass of spawn of a rose colour. Dissected it with Dr Grant. — It appeared very free from disease & had no intestinal worms; its back however was covered with small crustaceous animals. — Eyes small. — Hence probably does not inhabit deep seas? Stomach large. Liver without gall-bladder. Kidneys situated some way from the Vertebrae: an unusual fact in cartilaginous Fishes. — Air bladder was not seen. Brain very small; the optic nerves being nearly as large as the spinal cord, neither the brain or spinal matter

He also had extensive field notebooks from his voyage on the HMS Beagle.

His most famous notebook is his Red notebook where he put his most secret theoretical/speculative writing, including his early thoughts on evolution and natural selection, e.g.:

The same kind of relation that common ostrich bears to (Petisse. & diff kinds of Fourmillier): extinct Guanaco to recent: in former case position, in latter time. (or changes consequent on lapse) being the relation. — As in first cases distinct species inosculate, so must we believe ancient ones: [∴] not gradual change or degeneration. from circumstances: if one species does change into another it must be per saltum — or species may perish.

Make sense? Not really, unless you are willing to get not only hardcore steeped into Darwin's scientific world and what was known to it, believed by it, taken for granted by it, at dispute in it, and into the Darwiniana of Darwin himself (his own concerns, the references he is making, and being able to trace his own thought). Much less the particularities of 19th-century educated speech ("per saltum" = "by jumping"; he is saying that the changes from one species into another much be discrete, which, incidentally, is not what he would later argue when he said it happened very gradually).

Which is just to say: they are very copious and important primary sources, but they aren't at all transparent to a modern eye, even one steeped in modern scientific knowledge. This is part of the reason that "Darwin studies" are their own sub-genre in the history of science; the people who go full-on into Darwin tend to end up doing primarily just Darwin stuff. The work of Janet Browne, Adrian Desmond, James Moore, and other "dedicated Darwin scholars" are the place to turn for making sense to this, unless you really are willing to put in a lot of time.

If you are very interested in reconstructing Darwin's Beagle observations without slogging through all of that mess, Richard Keynes' The Beagle Record (Cambridge University Press, 1979) is the best option out there. It puts together a coherent account of the Beagle trip from Darwin's notes, letters, recollections, etc., and the diary of Robert FitzRoy (captain of the Beagle), and other accounts from people on the ship, including the often quite beautiful paintings by Conrad Martens, an artist who was on the ship. The sum of the sources gives one a very rich feeling of what it was like to be on the voyage (and to the fact that though Darwin is its most famous member, there were many others involved), and what it looked like through Darwin's eyes. It is a great book for someone interested in diving into Darwin. My only warning is that the paperback version is very inadequately printed (black and white, with muddy images and thin typesetting), compared to the (somewhat more expensive) hardback version.