NB: there are plenty of other places you can visit. These are just places we've visited and for which I have information and bird/mammal lists on this site. I'd especially like to recommend Ruma NP in western Kenya, which is undervisited and has lots of birds and mammals you're not so likely to see elsewhere, including Roan Antelope.
It has two hotels on the general tourist circuit, the Outspan, base hotel for Treetops and the Aberdares Country Club, base hotel for the Ark.
Treetops and The Ark are 'night viewing lodges' where salt is added to a natural salt lick at a waterhole and a variety of animals come down at night and are viewed by floodlights. The routine is that you check in at the base hotel and have lunch. You leave your main luggage at the base hotel and travel to the night lodge in a bus with your overnight bag. You have dinner at the night lodge and can stay up as long as you like to see what comes to the salt or water.
You have breakfast at The Ark then come down to Aberdares Country Club to collect your luggage and rejoin your main safari driver/guide, or be taken back to Nairobi. You can also stay over for another night, or longer, at The Ark.
At Treetops, only a few people stay for breakfast, most people breakfast at The Outspan.
You can also stay overnight or longer at The Outspan or Aberdares Country Club.
An additional interest of The Outspan is the small museum to Baden-Powell, founder of the International Boy Scout movement, as the building was his last home. His grave is in the grounds.
Famous for its elephants and wonderful views of Lake Kilimanjaro: if the clouds aren't totally covering the mountain.
Also excellent for birds because of the permanent marsh, even through the actual lake is usually dry. Conditions there are excellent for mirages.
It also has fine grey salt-sand which gets everyhwere as dust: in fact the name Amboseli means 'dust-bowl' in Maa. You'll get covered, so be aware of this if it's likely to be a problem. another interesting feature of this reserve are the frequent dust-devils.
The easiest way is to hire a car in town and drive in. Early morning is best (get a packed breakfast and aim to be there at first light). The forest has endemic species of bird, particularly the Sokoke Scops Owl, the Sokoke Pipit and some, like the Clark's Weaver which are rare elsewhere. It also has some unusual mammals, like the Golden-rumped Elephant Shrew, which incredibly we saw - on our own - by sheer luck.
Like all such habitats, it can be incredibly difficult to find the birds on your own, and I recommend you take one of the official guides. We went out with David Ngala, whom I highly recommend if he's still in the area. Not only did he find us two lovely red-phase Sokoke Scops Owls, but also took us to see the rare-in-Kenya African Pitta.
For a long time, the world record for species seen in 24 hours was held by Don Turner who used to be the Resident Ornithologist at the Lake Baringo Club, and was set from the Lodge.
The two main places on the Lake are the Club and Baringo Island Camp. We've stayed at both of them: they are quite different.
Lake Baringo Club is a large tourist-type lodge on the shore of the lake and is on the general safari circuit. Most visitors get a walk with one of the excellent resident ornithologists. You can usually choose to have a second trip for extra cost, and/or go out with the naturalist in a boat. The walks and boat trips are highly recommended: again, you won't see as many species on your own: but you will see plenty! The two walks which we did were one along the water's edge and the other along the base of the rift valley escarpment, two different habitats which predicably produced different birds.
Baringo Island Camp (on Ol Kokwe Island) has a totally different clientele and ambience. When we were there, the few othe visitors seemed to be Kenya residents or nationals out on R&R from Nairobi. It was a nice place to stay - very romantic, and also had an excellent resident naturalist. However, the island has fewer bird species - you can be taken on a boat trip to just offshore of the Lodge to 'up' your species tally.
We stayed at Delamere's Camp, where there were various activities included: the night drives were particularly good. If you have your own vehicle you can easily spend an afternoon at Lake Nakuru (another good chance to see large numbers of Flamingoes).
It's *well* off the normal tourist trail and is of particular interest to birders and butterfly enthusiasts. When we were there, we saw six of the last twelve African Grey Parrots in Kenya: I'm not sure what their current status is. You can either stay in Kakamega town and drive in (a less attractive option) or stay right in the forest in the Rondo Retreat Centre (where we stayed) or in a *very* basic (but very inexpensive) tree lodge nearby. The guides are based near the tree lodge and are very much worth their hire - excellent birders.
Be aware that although the reserve is teeming with game and predators during migration time, it can be disappointingly empty outside the migration period, when the game goes back to the Serengeti. Although the reserve looks small on a map, and indeed it is only the 'tip of the iceberg' of the Serengeti ecosystem, it is still a large area. If you're travelling in the migration time, check out where the animals will be and stay in a lodge in that area.
To be honest, outside the migration period, you could give the Mara a miss.
Mt Kenya also has its own 'native' flora and fauna. The main place to see these is at Mountain Lodge. Like the Aberdares, this is easily reachable from Nairobi, and is commonly an overnight stop on the way to/from the Samburu complex. You normally arrive around lunch time and stay for dinner and overnight and leave after breakfast. Again, most of the action takes place after dark and you can watch the animals at the waterhole by floodlights.
As an option in that area, you can stay at Naro Moru River Lodge. This is one of the base lodges used by people climbing the mountain, and that is its general ambience. They have a huge range of accommodation from camping in the grounds, through dormitories to really nice 'cottages'.
Here you can just wander the grounds on your own, looking for birds (a good place for Black Duck, for instance) and other creatures (I came across Colobus Monkeys and Duikers on an early-morning sortie), hire the bird guide (a good option as he knows where to look for each species and knows their calls). We stayed for a couple of nights, and on the middle afternoon we went down to Sweetwaters, which is another option for staying in this area.
The link is to Mountain Lodge. I don't have any pages on Naro Moru or Sweetwaters.
Most flights to e.g. the UK leave late at night, and most safaris aim to get you into Nairobi before lunch, so you can have a lot of hanging about to do. Much better to pre-arrange an afternoon in the National Park. Also, sometimes you don't start your safari directly on arrival in Nairobi, but have an afternoon to kill. If your schedule shows this, you can also pre-arrange to go into the park in the afternoon, or book through the tours desk at your hotel.
To be honest, you can easily spend a whole day (take a picnic) in Nairobi NP and not have seen everything. You can see all the main game except elephants and a good selection of the central plateau birds.
You can visit the National Park (see above) or the National Museum, Railway Museum, Bomas of Kenya (tribal dancing), or the Karen Blixen House and Giraffe Manor, usually a combined trip. You can pre-book these, but they can usually be booked from the tours desk at your Nairobi hotel.
There are several accommodations in the area: we've stayed at Lake Naivasha Country Club (a large, Block-owned lodge) and at Loldia House (owned by Governor's). Both are perfectly good. Loldia's is more expensive and much more exclusive; both have resident naturalists and you can go walks or boat trips on the lake. Other activities are available, particularly at Loldia, and you can also travel out to e.g. Lake Bogoria or Hell's Gate NP.
It's a different habitat than the other reserves, being semi-arid. As well as lots of elephants, which you can see drinking in and crossing the river, you can see some animals here that you won't see elsewhere in Kenya:
Grevy's Zebra - an attactive zebra, and a totally different species to the Plains Zebra which you'll also find here (they don't interbreed). Grevy's Zebras are highly endangered, and there are actually fewer Grevy's Zebra in Africa than there are Black Rhino.
Reticulated Giraffe, a particularly beautiful sub-species.
Gerenuk or giraffe-necked antelope, one of my favourites.
Also there are birds which you are much more likely to see here than elsewhere.
Shaba is a beautiful reserve, but is even hotter and dryer than Samburu/Buffalo Springs. Although the lodge there is a bit cheaper, I wouldn't recommend it for a first safari unless you have an articulable reason for going there. When we were there, we had to drive down to Samburu/Buffalo Springs each day (approx 30 mins) so that we'd see animals, since the animals had moved out of Shaba.
It is particularly famous for the relict population of Sable Antelope, for which this is the only location in Kenya. It has a lodge, the Shimba Hills Lodge.
The first safari we were on was a 'brochure' safari, and the first stop was Tsavo West. I'm sure this is because although it was impressive as a first stop, it would have been less so if it had come after such as Amboseli, Samburu and the Mara.
Probably worth leaving out of a safari out of Nairobi, particularly a first one. Tsavo East has Yellow Baboons, rather than the more usual Olive Baboons (separate species), good numbers of elephant and Kirk's Dikdik and a good chance of seeing Fringe-eared Oryx (which some, but not all, authorities consider to be a separate species).
General safaris are limited to a small (but still sizeable) proportion of the reserve.
It's a dry reserve, famous for giving visitors a reasonable chance of seeing African Hunting Dogs.
It's worth checking out where the migration will be during your visit and choosing accommodation accordingly: there's little point in being in the 'wrong area' as you'll have to spend time travelling into the 'right area' for your game drives: it's a vast area! It can also be worth sepnding several nights in the reserve, perhaps based at two lodges or camps.
Bear in mind that from mid July - late October most of the migration will be in the Masai Mara, in Kenya.
It's famous for elephants, but is also very good for birds. In fact, when we were there we saw learner guides getting some training in bird identification there.
If organising your own safari, it might be worth considering putting it at the beginning instead.
An absolute must is a dinner at New Emerson's in Stone Town (book from your own accommodation if you're not staying there).
The island has particularly spectacular snorkelling.
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