Book Hotels in Santee, NE

Cabins, apartments, houseboats! We offer comfortable & private vacation rentals

Save an extra 10% or more on select hotels with Member Discounts

Access exclusive hotel deals, only with the Travelocity app

Check prices for these dates

Next weekend
Jun 12 - Jun 14
In two weeks
Jun 19 - Jun 21

Filter by

Guest rating
Guest rating
Star rating
Payment type
Payment type
Property type
Property type
Neighborhood
Neighborhood
Traveler experience
Traveler experience
Popular locations
Popular locations
Meal plans available
Meal plans available
Property amenities
Property amenities
Accessibility
Accessibility

Top Santee hotels

Beautiful log cabin, only 1.7 miles from lake dock by Lewis & Clark, Yankton SD

Beautiful log cabin, only 1.7 miles from lake dock by Lewis & Clark, Yankton SD

Yankton SD
This cabin featured laundry facilities and barbecue grills.
"It was a wonderful property about a 5 minute drive to marina. Lots of wildlife. Property was well stocked and clean. Plenty of room for everyone. The one negative was that there is no television in the living room. So if you want to watch a game or movie as a group, there is no larger space with ..."

Reviewed on Aug 6, 2025

Get rates
Opens in a new windowBeautiful log cabin, only 1.7 miles from lake dock by Lewis & Clark, Yankton SD
Modern Lewis and Clark lake home with lake views and 3 min drive to the beach!

Modern Lewis and Clark lake home with lake views and 3 min drive to the beach!

Crofton NE
$950 nightly
The price is $1,050 total per night from Jun 10 to Jun 11
$1,050 total
Jun 10 - Jun 11
Total with taxes and fees
This vacation home includes a garden and laundry facilities.
"Beautiful home plenty, of space, lots of refrigerator room! Great for our big family. Would love to rent it again in the future! My favorite time was sitting on the deck in the evening."

Reviewed on May 10, 2026

Opens in a new windowModern Lewis and Clark lake home with lake views and 3 min drive to the beach!
Newly Remodeled Creekside Bungalow on 3 acres with private Beach/Creek access

Newly Remodeled Creekside Bungalow on 3 acres with private Beach/Creek access

Verdigre NE
$215 nightly
The price is $238 total per night from Jun 8 to Jun 9
$238 total
Jun 8 - Jun 9
Total with taxes and fees
Stay at this vacation home in Verdigre. Enjoy air conditioning.
"It’s a cute little house! It’s easy to find but far enough away from people. Definitely going to save it for when I’m ever out that way!"

Reviewed on May 10, 2026

Opens in a new window Newly Remodeled Creekside Bungalow on 3 acres with private Beach/Creek access
Cozy cabin near Lewis and Clark Lake and CJ’s at the Lake

Cozy cabin near Lewis and Clark Lake and CJ’s at the Lake

Crofton NE
Stay at this cabin in Crofton. Enjoy air conditioning. Popular attractions Deep Water Recreation Area and Lewis and Clark Lake State Recreation Area are located ...
"Very nice cabin, very great location, we had a good time there, everyone there very friendly, planning on conning back again"

Reviewed on Oct 26, 2025

Get rates
Opens in a new windowCozy cabin near Lewis and Clark Lake and CJ’s at the Lake
Lewis & Clark Trail Hideaway, SD side / 2 min to the lake / 10 min to Yankton.

Lewis & Clark Trail Hideaway, SD side / 2 min to the lake / 10 min to Yankton.

Yankton SD
A hot tub is featured at this vacation home, along with a garden and laundry facilities. Barbecue grills are provided for your convenience.
"The backyard of this property is beautiful and so quiet! We enjoyed the hot tub every night. It’s very close to the park so we hiked and had a picnic by the lake. There are a lot of fun board games and lots of kitchen appliances if you enjoy cooking. Overall, a great stay. Would definitely ..."

Reviewed on May 31, 2026

Get rates
Opens in a new windowLewis & Clark Trail Hideaway, SD side / 2 min to the lake / 10 min to Yankton.
ThePinecone - luxury vacation rental awesome deck with view & amenities for 2-18

ThePinecone - luxury vacation rental awesome deck with view & amenities for 2-18

Yankton SD
A hot tub is featured at this vacation home, along with limo/town car service and a garden. Families will appreciate the playground and onsite laundry facilities. ...
"This property was beautiful and quiet and had a great view of the lake and wildlife."

Reviewed on May 11, 2026

Get rates
Opens in a new windowThePinecone - luxury vacation rental awesome deck with view & amenities for 2-18
Haven by the Lake

Haven by the Lake

Yankton SD
This vacation home features a garden, laundry facilities, and barbecue grills.
"Lindsey was such a great host. She got back to me right away with a couple questions I had. I really appreciate that. I love all of the extras they have there for us to do use!!"

Reviewed on May 27, 2026

Get rates
Opens in a new windowHaven by the Lake
Lewis and Clark Resort

Lewis and Clark Resort

2.5 out of 5
43496 Shore Drive Yankton SD
$114 nightly
The price is $120 total per night from Jun 7 to Jun 8
$120 total
Jun 7 - Jun 8
Total with taxes and fees
A marina and a restaurant are featured at this hotel. Traveling on business? Take advantage of the free WiFi in public areas, conference center, and conference ...
"We liked everything they had to offer peaceful walks lake very beautiful would suggest renting cart for ride thru parks enjoyed it very much ! Seen dear in campground had our puppy with us very friendly service!! Will stay there again!!!"

Reviewed on Jun 5, 2026

Opens in a new windowLewis and Clark Resort
Hunters & outdoor lovers charming 4-bedrm lake house with best view on the lake!

Hunters & outdoor lovers charming 4-bedrm lake house with best view on the lake!

Crofton NE
This cabin includes a garden and laundry facilities.
Get rates
Opens in a new windowHunters & outdoor lovers charming 4-bedrm lake house with best view on the lake!
Don't see what you're looking for?
See all available properties in Santee
View all properties
Lowest nightly price found within the past 24 hours based on a 1 night stay for 2 adults. Prices and availability subject to change. Additional terms may apply.

Frequently asked questions

What are the top kid-friendly hotels in Santee?
From cool amenities to extra space, kid-friendly hotels come with features that can help transform a routine family vacation into a sensational one. These Santee options make vacationing with your youngsters child's play: The whole team will enjoy their time at Private updated hunting lodge/farmhouse. Pet-friendly facilities and a barbecue grill are just a few of the things that help make this property a favorite. Bear Historic Home is another excellent choice. After an exciting day of exploring, come home to your cozy room and amenities like a king bed and animal viewing activities.
Where can I find cheap hotels in Santee?
At Travelocity you'll find really nice hotels in Santee at great prices. We source incredible prices with our trusted partners, so you have a tempting selection of cheap hotels to choose from. If you can be flexible on dates and location, consider staying at a hotel near Santee rather than in Santee. We may find you even better rates, too.
How do I find the best Santee hotel deals?
Simple! On Travelocity, look through the fantastic offers we've already found in Santee then use our filters to find a great deal that's perfect for you. Enter your travel dates, select the number of rooms you need, and we'll do the rest. You can get great discounts on flights and car hire, too, when you bundle.
How much does it cost to stay in a hotel in Santee?
The cheapest hotel in Santee is $120. This price was available within the past 7 days, for stays with a check-in date within the next year. Of course, the price you pay depends on your dates of travel, the length of your stay, and the hotel's location. Prices and availability are subject to change. Additional terms apply.
How many hotels are in Santee?
There are 64 hotels in Santee on Travelocity.
What are the best hotels in Santee?
Santee has so many great hotels to choose from at Travelocity — and it's so easy to find the perfect one. Just choose one of our popular pre-selected hotels with great reviews, or you can refine your search to build your ideal stay. Simply filter hotels based on price or star rating, or select properties with a pool, a hot tub, or a range of other amenities and pick the best place to stay in Santee for you!
When is the best time to visit Santee?
If you want the joy of a fun-filled trip in peak season, visit Santee during May, July and August. If you'd prefer the peace of off-season, book a stay during quieter months, such as November, December and January.
When is the cheapest time to stay in Santee?
Based on historic data is usually the cheapest month to visit Santee. However, we have incredible deals all year round, so we're confident you'll find a room in your budget whenever you choose to travel.
Are there any great family-friendly hotels in Santee?
There are multiple hotels in Santee that will please the whole family. Do you need adjoining rooms, babysitting services or a swimming pool? We've got you covered. Use our family filter to narrow your search down and use guest reviews to help you pick the perfect place for your next family trip to Santee. We have plenty of kid-friendly hotels in Santee to choose from on Travelocity!
Why book a hotel in Santee through Travelocity?
Because we have the top hotels in Santee! We want to help you travel more and worry less. That's why we've put the most amazing hotel, car rental, and flight deals in one place. When you search for hotels with us, you know you're getting fantastic prices with no hidden fees and free cancellation on most properties up to 24 hours before your stay. If you become a Travelocity member, you also get exclusive member discounts. Sign up today!
How do I cancel my hotel booking in Santee on Travelocity?
Canceling your booking with Travelocity is easy. Sign into your account and select My Trips. Here, you will see your cancellation options. We offer free cancellation on many properties.

Recent Santee hotel reviews by fellow wanderers

Lewis and Clark Resort

Lewis and Clark Resort

5 out of 5
Posted 18 hours ago
Travelocity Verified Review
"We liked everything they had to offer peaceful walks lake very beautiful would suggest renting cart for ride thru parks enjoyed it very much ! Seen dear in campground had our puppy with us very friendly service!! Will stay there again!!!"
A verified traveler stayed at Lewis and Clark Resort
Lewis and Clark Resort

Explore More Ways to Travel with Travelocity