Book Hotels in Henderson Harbor, NY

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

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
Amenities
Amenities
Accessibility
Accessibility

Top Henderson Harbor hotels

The GillHouse

The GillHouse

2 out of 5
13565 County Rte 123 Henderson Harbor NY
A restaurant and a bar/lounge are featured at this hotel. Guests will appreciate free perks like free self parking and WiFi in public areas. A snack bar/deli ...
Clean room

Reviewed on Nov 10, 2025

Get rates
Opens in a new windowThe GillHouse
Holiday Inn Express Hotel & Suites Watertown-Thousand Island by IHG

Holiday Inn Express Hotel & Suites Watertown-Thousand Island by IHG

2.5 out of 5
1290 Arsenal St Watertown NY
Fully refundable
$105 nightly
The price is $117 total per night from Feb 18 to Feb 19
$117 total
Feb 18 - Feb 19
Total with taxes and fees
A restaurant and an indoor pool are featured at this hotel. Traveling on business? Take advantage of the business center and free WiFi in public areas. Guests ...
Clean room

Reviewed on Feb 9, 2026

Opens in a new windowHoliday Inn Express Hotel & Suites Watertown-Thousand Island by IHG
Fairfield Inn & Suites Watertown Thousand Islands

Fairfield Inn & Suites Watertown Thousand Islands

2.5 out of 5
250 Commerce Park Dr Watertown NY
Fully refundableReserve now, pay when you stay
$124 nightly
The price is $138 total per night from Feb 16 to Feb 17
$138 total
Feb 16 - Feb 17
Total with taxes and fees
This hotel features an indoor pool and a 24-hour gym. Traveling on business? Take advantage of the 24-hour business center and free WiFi in public areas. Guests ...
The staff was very friendly and welcoming.

Reviewed on Feb 1, 2026

Opens in a new windowFairfield Inn & Suites Watertown Thousand Islands
Hilton Garden Inn Watertown/Thousand Islands

Hilton Garden Inn Watertown/Thousand Islands

3 out of 5
1290 Arsenal Street Watertown NY
Fully refundableReserve now, pay when you stay
$116 nightly
The price is $128 total per night from Mar 13 to Mar 14
$128 total
Mar 13 - Mar 14
Total with taxes and fees
This hotel features an indoor pool, a hot tub, and a restaurant. Traveling on business? Take advantage of the free WiFi in public areas, conference center, and ...
Beautiful luxurious Room 👍

Reviewed on Feb 3, 2026

Opens in a new windowHilton Garden Inn Watertown/Thousand Islands
Hampton Inn Watertown

Hampton Inn Watertown

2.5 out of 5
155 Commerce Park Dr Watertown NY
Fully refundableReserve now, pay when you stay
$98 nightly
The price is $108 total per night from Feb 21 to Feb 22
$108 total
Feb 21 - Feb 22
Total with taxes and fees
This hotel features an indoor pool and a gym. There's no skimping on freebies - guests receive free buffet breakfast, free WiFi, and free self parking. A 24-hour ...
Very clean rooms. Staff was very friendly and helpful. I booked two rooms and without asking they made them adjoining rooms which really was helpful. Even the breakfast was good. Typical waffle machine, eggs, bacon, type stuff. Everyone was super nice.

Reviewed on Feb 9, 2026

Opens in a new windowHampton Inn Watertown
Days Inn by Wyndham Watertown Fort Drum

Days Inn by Wyndham Watertown Fort Drum

2 out of 5
25940 US Route 11 Calcium NY
Fully refundableReserve now, pay when you stay
$48 nightly
The price is $53 total per night from Mar 1 to Mar 2
$53 total
Mar 1 - Mar 2
Total with taxes and fees
This hotel doesn't skimp on freebies - guests receive free continental breakfast, free WiFi, and free self parking. Traveling on business? Take advantage of ...
Staff very friendly, clean, comfortabe room. Could use some better pillows.

Reviewed on Feb 12, 2026

Opens in a new windowDays Inn by Wyndham Watertown Fort Drum
Comfort Inn & Suites Watertown - 1000 Islands

Comfort Inn & Suites Watertown - 1000 Islands

2.5 out of 5
110 Commerce Park Drive Watertown NY
Fully refundableReserve now, pay when you stay
$80 nightly
The price is $89 total per night from Feb 22 to Feb 23
$89 total
Feb 22 - Feb 23
Total with taxes and fees
This hotel features an indoor pool and a gym. Traveling on business? Take advantage of the business center, free WiFi in public areas, and free airport shuttle. ...
Clean, nice staff! Some parts of building a little out dated.

Reviewed on Feb 4, 2026

Opens in a new windowComfort Inn & Suites Watertown - 1000 Islands
Quality Inn & Suites Watertown Fort Drum

Quality Inn & Suites Watertown Fort Drum

2.5 out of 5
8000 Virginia Smith Drive Calcium NY
Fully refundableReserve now, pay when you stay
$55 nightly
The price is $61 total per night from Feb 22 to Feb 23
$61 total
Feb 22 - Feb 23
Total with taxes and fees
This hotel doesn't skimp on freebies - guests receive free continental breakfast, free WiFi, and free self parking. Business travelers can take advantage of ...
Only complaint we have is that a king size bed should have king sized pillows. The couch cushions the use are a joke for sleeping.

Reviewed on Feb 13, 2026

Opens in a new windowQuality Inn & Suites Watertown Fort Drum
Ramada by Wyndham Watertown/Thousand Islands NY

Ramada by Wyndham Watertown/Thousand Islands NY

2.5 out of 5
21000 NY State Rt 3 Watertown NY
Fully refundableReserve now, pay when you stay
$65 nightly
The price is $72 total per night from Feb 22 to Feb 23
$72 total
Feb 22 - Feb 23
Total with taxes and fees
This hotel features a 24-hour gym and a seasonal outdoor pool. Traveling on business? Take advantage of the 24-hour business center and free WiFi in public areas. ...
Easy check in and check out, the room was clean.

Reviewed on Feb 6, 2026

Opens in a new windowRamada by Wyndham Watertown/Thousand Islands NY
Don't see what you're looking for?
See all available properties in Henderson Harbor
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 Henderson Harbor?
Family trips are where amazing memories are made, but traveling with little ones can be a challenge. These kid-friendly Henderson Harbor hotels come with perks that aim to keep young and old alike comfortable and happy: The whole team will love staying at The Cottage at Rays Bay · Cottage with hot tub and gorgeous sunsets!. A travel crib and a king bed are among the things that help make this property a sought-after option. Also look into Lake Ontario (Henderson, NY). It offers a deck, a king bed and lots of opportunities for precious family time.
Where can I find cheap hotels in Henderson Harbor?
At Travelocity you'll find really nice hotels in Henderson Harbor 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 Henderson Harbor rather than in Henderson Harbor. We may find you even better rates, too.
How do I find the best Henderson Harbor hotel deals?
Simple! On Travelocity, look through the fantastic offers we've already found in Henderson Harbor 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 Henderson Harbor?
The cheapest hotel in Henderson Harbor is $53. 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 Henderson Harbor?
There are 186 hotels in Henderson Harbor on Travelocity.
What are the best hotels in Henderson Harbor?
Henderson Harbor 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 Henderson Harbor for you!
When is the best time to visit Henderson Harbor?
If you want the joy of a fun-filled trip in peak season, visit Henderson Harbor during June, 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 Henderson Harbor?
Based on historic data is usually the cheapest month to visit Henderson Harbor. 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 Henderson Harbor?
There are multiple hotels in Henderson Harbor 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 Henderson Harbor. We have plenty of kid-friendly hotels in Henderson Harbor to choose from on Travelocity!
Why book a hotel in Henderson Harbor through Travelocity?
Because we have the top hotels in Henderson Harbor! 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 Henderson Harbor 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 Henderson Harbor hotel reviews by fellow wanderers

Days Inn by Wyndham Watertown Fort Drum

Days Inn by Wyndham Watertown Fort Drum

5 out of 5
Posted 2 days ago
Travelocity Verified Review
"Staff very friendly, clean, comfortabe room. Could use some better pillows."
A verified traveler stayed at Days Inn by Wyndham Watertown Fort Drum
Days Inn by Wyndham Watertown Fort Drum

Explore More Ways to Travel with Travelocity