The Galapagos Islands have a highly variable climate, as does Ecuador's mainland. There are two seasons in the islands: the hot/rainy season from December to June, and the cooler season from June to November.

In the hot season, from December to June, the humidity is high, and the average temperatures are in the 80s F (26°-30°C). There may be occasional showers, but the days are generally warm and sunny.

In the cooler season, from June to November, you can expect cool winds, occasionally bringing with them a light misty-type drizzle called "garúa." Temperatures average in the 70s °F (20–24°C) during the day and lower at night.

Each month brings unique climate variations and wildlife viewing opportunities. Peak season for naturalist tours is typically December through May when the seas are the calmest and the weather the warmest. However summer months June, July and August are also very popular as the animals are more active. September through November is typically low season when most boats will leave the islands for dry dock. For divers peak season is from July to November, when whale sharks can be found at Wolf & Darwin.

Flights to the Galapagos are relatively easy to arrange and depart from Quito and Guayaquil on a daily basis for the Isla Baltra Airport, about an hour by taxi and ferry from Puerto Ayora (the main settlement of the Galapagos) on the central island of Santa Cruz. There are also daily flights to San Cristóbal. The airport is a 20-minute walk (5-minute taxi) from the center of Puerto Baquerizo Moreno, and lies within the town.

Flights from Guayaquil are slightly less expensive than from Quito; however, there is more availability from Quito as there are typically two flights a day from Quito and only one from Guayaquil.

Avianca and LATAM Airlines have flights to the Galapagos. The price varies a bit between companies, for foreigners around US$457 from Quito in low season, or $505–512 in high season (July, August and December) and less from Guayaquil, $419 low season to $522 in high season. Ecuadorians pay almost half the price and there is a 20% discount on Aerogal flights if you have an ISIC studentcard.

Inter-island flights are available from EMETEBE Airlines, which operates nine seater aircraft to transport passengers and their luggage from San Cristobal Airport to Isabela, Santa Cruz and Baltra islands. Bookings can be done directly through EMETEBE's website or a travel agent.

Private yachts can arrive into any of the five ports in Galapagos while in transit and remain at that port for a maximum of 21 days. Boats wishing to visit more than one site or cruise the islands may do so but only by special permit from the national park and by working with a licensed yacht agency.

There are cargo boats that travel to the Galapagos each week. However, these boats are not allowed to take travelers on board.

Seeing the sites and wildlife of the Galapagos is best done by boat, just as Charles Darwin did it in 1835. Over 60 cruise ships ply the Galapagos waters - ranging in size from 8 to 100 passengers. Most people book their place well in advance (as the boats are usually full during the high season). Be sure the agent through whom you book is a Galapagos specialist with a good knowledge of a wide variety of ships. This will ensure that your particular interests and/or constraints are matched with the ship most suitable to them.

There are a lot of companies that can book accommodation on a Galapagos tour either in Puerto Ayora or from Guayaquil or Quito. While it is possible to get a last-minute deal, be aware that many budget tours may spend extra time in Puerto Ayora, might not have the best boats, and may only visit the inner islands. Last minute 4-day cruises can be organized in Puerto Ayora for $400–1800. The widely used GalapagosCruiseLinks site can give you an idea of last-minute prices for a range of ships sailing within the next 90 days.

When looking for a tour consider the following:

• Number of passengers. The national park restricts the size of the boats allowed to cruise the islands, with some islands such as Genovesa being limited to boats with no more than forty passengers. Though the maximum size boat permitted to cruise the islands is 100 passengers, as you might imagine 100 people showing up on a beach all at the same time can be overwhelming to the local wildlife. All passengers will be divided up into a maximum group size of 16 passengers per naturalist guide. Therefore it is generally best to travel on a boat with fewer passengers (between 16 and 32 passengers is ideal).
• Itinerary. The National Park sets all of the cruise itineraries. Each itinerary is designed to have a mixture of habitats and show case the diversity of the islands by combining the Southern Espanola and Floreana, Central, Western Fernandina, Isabela or Northern Genovesa Islands. Most boats will visit 2 or 3 of these areas during a week.
• Availability. Most of the best cruises are booked up months in advance, so best to book early. The last 2 weeks of December are often booked solid a year in advance on many ships, while few ships sail at full capacity during the first two weeks of December.
• Level of activity. Visits to the islands are only permitted during the twelve hours of daylight 06:00-18:00. Typically a cruise will have two excursions each day, a morning and an afternoon that will be a combination of shore and water excursions. Walks are generally at a slow pace offering plenty of time for interpretation and photos. The landings may be slippery and some trails can be rocky, which makes them difficult for people with mobility or balance problems, but in general the walks are easy. Water excursions may include snorkeling, kayaking, panga rides (rides in local dinghies), and rides in a glass-bottom boat, depending on your cruise. Life under the water is more diverse than that on shore and snorkeling with sea lions is frequently the highlight of the trip for many visitors.
• Additional costs. Many tours do not include the $100 park entry fee or the cost of a flight from the mainland to the islands (about $500 from Quito), and a $20 INGALA Tourist Control Card. Less expensive boats may also charge for beverages, use of snorkel equipment, wetsuits and kayaks.
• Time spent in the islands. The cruise length includes the day you arrive and the day you depart the Galapagos. Flights typically arrive the islands around noon time or in the early afternoon and leave the islands about the same time. On your first day you will typically have one excursion, and on the day you leave you may or may not have an excursion. In addition, all eight-day cruises are required to visit the town of Puerto Ayora and the Charles Darwin Research Station on Santa Cruz. Many itineraries will combine this day with a visit to see the tortoises in the wild in the highlands of Santa Cruz. Shorter cruises will take advantage of the close proximity of the Baltra airport to Puerto Ayora and let passengers who boarded the cruise in San Cristobal leave the cruise in Santa Cruz or vice versa.
• Type of boat. Quality of boats varies widely. Less-expensive tours use boats that may not be capable of traveling as quickly between islands, be as comfortable, or be as well-maintained. You generally get what you pay for.

While the majority of the islands will be off-limits without a guide, it is possible to travel via speed boat between the towns on San Cristóbal, Santa Cruz and Isla Isabela. Trips to Floreana can also be arranged. Speed boats cost $30 one-way, or $50 both ways with an open return date. Each of these islands offers the possibility of joining organized local daytrips or of traveling on your own while within the town limits.

Hotels and hostels are available on each of these islands from $10–500, while hotels along the water are generally full especially in Santa Cruz. During peak season (Christmas & Easter weeks) as well as during special events, all hotels are frequently sold out well in advance. However, if you are traveling at other times of the year, you may be able to find availability by just showing up.

From Santa Cruz it is possible to book day trips to the uninhabited islands of North Seymour, South Plazas, Santa Fe and Bartolome. Advance reservations are normally required; however, on occasion you can find space due to a last-minute cancellation the night before.

Ship-based trips to Galapagos are considered to be the optimal way of getting out and about in the archipelago, allowing you to maximize your exposure to what the islands are famous for. Land-based tours have grown dramatically since the early 1990s when very few tourists came to Galapagos without taking a cruise. In 2017 while approximately 72,000 people enjoyed a cruise every year, over 150,000 land-based visitors came to the islands on island-hopping trips. Land-based visitors trade off the opportunity to travel around to remote parts of the archipelago and the convenience of waking up at a new destination every day, for the cheaper cost. While ship-based tourism is strictly regulated, with a cap on the total number of ship-based beds available, land-based tourism is unregulated. Between 2009 and 2015, it grew at an annual rate of 14%. More and more agencies are offering organized island-hopping land-based trips - these are easily found on-line. Some visitors opt for a self-guided trip, booking their accommodations and day excursions directly.

Cruises are the only option to see the majority of remote islands. All cruise ships are required to have a certified naturalist guide. Each cruise ships has a fixed itinerary for the year which is set by the Galapagos National Park, with the purpose being to control the number of tourists arriving at any time on each island. Cruises are available in 2-, 4-, 5-, 8- and 15-day options. The following is a list of typical sights:

• Climb the hill on Bartolome for the classic Galapagos view
• Visit the Giant Tortoise breeding and rearing program at the Charles Darwin Research Center on Santa Cruz.
• See the red neck sacks of the Magnificent Frigatebird on North Seymour or El Junco, San Cristobal.
• Visit unique species like the Galapagos penguins on Isabela or Floreana.
• Go snorkeling with sea lions and pacific sea turtles.

Snorkeling and diving are very popular activities as the sea life is so rich and colourful.

Snorkeling equipment should be available from your tour operator (but check first) if you don't have your own. You may also want to bring a waterproof camera. Remember to wear at least a T-shirt and sunblock if you are snorkeling, as it's all too easy to get sunburnt in the strong sun. Snorkeling offers a way to be in the water with fish, sea turtles, sea lions, and other creatures and is a great option for those who don't have scuba certification. The islands that are older (further to the west) often have cold temperatures. Wetsuits can be rented at the same locations as snorkeling equipment.

Diving in the Galapagos is incredible, as noted by Rodale's Scuba Diving Magazine. Darwin and Wolf Islands have been ranked as the best dive destination in the world for several years in the categories of healthiest marine environment, best big animal dive and best advanced diving. That said, the Galapagos is not necessarily the right place for beginners or novices. Currents, surge, cold water, and sometimes poor visibility and depths make this a challenge. Certification courses are available in both Santa Cruz and San Cristobal for those looking to learn, and there are several dive sites that are relatively beginner-friendly.

There are 2 ways to dive in the Galapagos Islands:

1. Daily dives with a local tour operator from Santa Cruz, Isabela and San Cristobal.
2. Galapagos liveaboards. Only liveaboards reach Darwin and Wolf. These 2 sites are the reason most divers come to Galapagos.

Two of the world's premier diving destinations, Darwin Island and Wolf Island, are accessible only via live-aboard cruises. These islands present challenging currents and are not suitable for beginners, but offer amazing opportunities to see huge schools of hammerhead sharks, Galapagos sharks, Silky sharks and whale sharks in season (July-Nov), in addition to other pelagic life like giant mantas, eagle rays, sting rays, huge schools of jack and tuna, sea turtles, sea lions and more.

Park regulations may change unexpectedly. In 2007, many divers were caught unaware as the National Park withdrew diving permits from quite a few cruise ships without notice, leaving many divers without dive cruises they had booked far in advance. For this reason, travellers are advised to get the most up-to-date information possible when planning a dive trip to the Galapagos Islands. In 2010, the National Park began regulating land-based diving, and few of the many shops operating had the necessary permits. It is best to ask if an operator has a dive permit, otherwise you may be turned back by Park Rangers and not permitted to dive. In 2011, the National Park stopped allowing dive live-aboards to offer land visits, except for the Highlands of Santa Cruz, which is on all itineraries.

You can fish in the Reserve, for marlin, tuna, wahoo and many other species but only if you are using an operator and boat that have the requisite Artisanal Vivencial Fishing licences issued by the Galapagos National Park. "Sport Fishing", as such, is prohibited. The Galapagos National Park publishes a list of Vivencial Fishing licence-holders and their boats, but they do not keep the list up to date.

When Vivencial Fishing, you can keep a limited quantity of fish for personal consumption but all marlin must be released unharmed.

Vivencial Fishing was conceived with the purpose of providing local fishermen with an ecologically sustainable alternative to commercial fishing. However, there is constant pressure, both political and commercial, to legalize sport fishing and open the market to better financed and better connected outsiders.

Hiking is often included as part of organized cruises or tours of the highlands. Although you will often see fewer animals during these tours, you will often gain a greater understanding of the difference in terrain and vegetation as well as the formation of the islands. Hiking is restricted in all National Park land; however, several sights, like the Wall of Tears on Isabela and Cerro Tijeras on San Cristobal can be hiked independently. The rules are that a guide must accompany all groups of more than eight people in the National Park.

Biking provides quicker access to far sites from the ports. Bike rentals are available on Isabela, San Cristobal and Santa Cruz for around $15 per day.

The Galapagos provides some good waves and many locals make it a daily activity. Boards can be rented by the day or month at port towns. In general sites are marked with a place to rest surf boards as to not damage the land. The following are beaches that allow surfing:

• Punta Carola, San Cristobal
• La Loberia, San Cristobal
• Tongo Reef, San Cristobal
• Tortuga Bay, Santa Cruz
• Playa Ratonera, Santa Cruz
• Isabela has a more continuous sandy shoreline that provides open surfing, larger waves are at the end of the road that follows the beach in the opposite side of the port
• The Galapagos Surf Co. The only surf travel company in the Galapagos. Waves are available not only in San Cristobal with north swell, but also in Santa Cruz and Isabela islands as well. 

To minimize the impact of sightseeing on the unique ecosystem and mitigate issues with introduced species, several organizations provide conservation-based volunteering.

• Hacienda Tranquila works on environmental, community and social issues. Volunteers stay on the grounds and cook for themselves. The hacienda is owned and managed by locals.
• Hacienda Esperanza works to conserve the environment and promote sustainable technologies. Volunteers are provided room and board as part of volunteering. The hacienda is owned and managed by locals.
• Jatun Sachu^{[dead link]} works to conserve the Galapagos and covers a larger area. Volunteers are provided room and board as part of volunteering.
• Fundacion Bolivar Education^{[dead link]} has a conservation farm project on San Cristobal, as well as a habitat restoration project. Teaching programs in the islands include Alejandro Alvear School and Teaching Support at a local school.

Kayaking allows you to navigate more of the water without a boat. Kayaks can be rented at Tortuga Bay in Santa Cruz and the port at San Cristobal to navigate the nearby beaches. Fish and sea turtles can often be seen while kayaking; however, conditions should be checked before renting.

Horseback riding can be organized to allow you to see the highlands in greater detail. Tours are roughly $50. Additional tours may be found through taxis or local tour agencies.

The codified park rules are:

1. To visit the National Park you must always be accompanied by a certified Galapagos National Park guide.
2. Galapagos is a unique and fragile environment. Take only photographs and video. Professional shooting needs authorization from the National Park.
3. Stay within the limits of the walking trails, for your safety and that of the flora and fauna.
4. To avoid affecting the wildlife's natural behavior, avoid getting closer than two meters to the animals.
5. Camping is allowed only at specific sites. If you wish to camp, you must first obtain a permit from the Galapagos National Park.
6. Help conservation by cooperating with the authorities in their inspection, monitoring and control duties. Report any anomalies to the National Park.
7. Do not introduce foreign organisms to the islands, as these can have a negative impact on the ecosystem.
8. Do not buy souvenirs which are made from black coral, sea shells, sea lion teeth, tortoise shell, volcanic rock or endemic woods.
9. Galapagos animals have their own feeding behavior. Never feed the animals. Feeding them can be detrimental to their health.
10. Galapagos landscapes are beautiful and unique. Do not spoil them by writing or etching rocks or trees.
11. Do not litter while on the islands. Always dispose of rubbish in a safe and appropriate way.
12. Smoking or making camp fires in the national park areas is forbidden and can cause devastating fires.
13. Fishing is strictly forbidden, except on those boats specifically authorised by the Galapagos National Park.
14. Jet skiing, submarines, water skiing, and aerial tourism are all forbidden.