Big Lagoon or Small Lagoon: Which El Nido Lagoon to Choose

Head to head

Everything below comes from the tour listings themselves and from visitor guides who timed their own visit. The fee is identical, the kayak rate is close, and every real difference sits in the last three rows: how long you need inside, how many boats are there with you, and what happens when the day is full.

One more lagoon that confuses the comparison

Two other names come up in the same conversation and neither is the Small Lagoon. The Secret Lagoon is a Tour A stop, reached by wading or swimming through a hole in the rock face, and no separate fee is stated for it on the listings here. Cadlao Lagoon is a Tour D stop with no separate fee stated either, and it is the one people mean when they say Tour D has two lagoons.

So a Tour A ticket buys the Big Lagoon and the Secret Lagoon, one of which is paid and one of which is not. A Tour D ticket buys the Small Lagoon and Cadlao Lagoon, again one paid and one free. If someone tells you they did the Small Lagoon on Tour A, they either did the Secret Lagoon or they went before the routes were rearranged.

Three parts, and the clock

The lagoon has an inlet, a main body and a left arm. The inlet is the narrow mouth where boats anchor and kayaks are hired, and it is the busiest water in Bacuit Bay on a fine morning. Past it the lagoon opens into the main part, and visitor guides who timed the paddle put fifteen minutes on that leg alone. The left arm has sharp coral at its entry, so it rewards care rather than speed.

Allow about 90 minutes to see the whole thing without turning around early. That number matters because it is longer than most stops on a joiner boat: one Tour A listing publishes 105 minutes at the Big Lagoon, which fits, while a combo day squeezing 7 to 8 stops into eight hours does not. What that means for a two-route day is covered in the combo tours page.

Getting in, and what can stop you

Entry is limited. Visitor guides report the municipality capping the lagoon at 400 visitors a day with allocated time slots, the earliest at 7:00 am and each slot around 90 minutes, and one guide's account of the system is worth reading before you book. Those figures are what guides report, not a line in a published ordinance, so treat them as the shape of the system rather than the letter of it.

The hard fact is on the listing itself. The most-reviewed Tour A here states that entry to the Big Lagoon is limited and that if entry is no longer available you will visit a different spot. That is the operator's own wording, and it is the sentence to plan around: on a busy day in season a Tour A boat can be rerouted, and the ticket does not owe you the lagoon. The shared Tour A with the Big Lagoon prints the same caveat in its inclusions.

Swimming, and what the water is like

None of the listings compared here states a swimming ban inside the lagoon, and reviewers describe swimming from their kayaks once past the inlet. Two practical limits apply anyway. The inlet is a working channel with kayaks and tenders moving through it, so it is the wrong place to be in the water. And the distance from the anchorage to the far end is longer than it looks from a boat, which is exactly why kayaks are hired at the mouth rather than optional.

The floor shelves from ankle-deep gravel at the entrance to deep green water in the middle. Reviewers mention jellyfish at the lagoons in some months, which is a rash guard problem rather than a cancellation, and the rest of the water hazards sit on the safety and restrictions page.

A narrow gap and shallow water

You enter through a narrow gap in the rock wall, low enough that a kayak is the sensible way through it and shallow enough inside that paddling beats swimming for covering ground. Beyond the gap the pool opens out under overhanging cliffs, with small archways at the edges that reviewers on the shared Tour D describe paddling through.

The scale is the difference. Where the Big Lagoon is a corridor you travel down, the Small Lagoon is a room you move around in, and 45 to 60 minutes is enough to see all of it. The fee is the same ₱200, and the kayak is where the listings disagree: one Tour D listing prices a two-seater at about ₱300 an hour, another puts a two-seat kayak at ₱350 and a three-seater at ₱500. Either way it is the same cash-on-the-water arrangement as Tour A.

The boats around you

Tour D is the least-sold of the four routes and the closest to town, and both facts show up in the water. Reviewers on the shared Tour D with the Small Lagoon and Cadlao count fifteen to seventeen people on their boat and describe being alone at both lagoons, which is not a sentence anyone writes about the Big Lagoon in high season.

The trade is scenery on a smaller scale and a route with fewer showpiece stops. Tour D fills the rest of its day with Cadlao Lagoon, Pasandigan Cove, Paradise Beach, Nat Nat for snorkelling and one more beach depending on the operator. It is the route people book second, after Tour A has shown them what a busy stop feels like, and the one seasoned repeat visitors book first.

One route each, since the routes were redrawn

A municipal ordinance moved the Small Lagoon from Tour A to Tour D on carrying-capacity grounds, and the history of that decision belongs to the guide to which El Nido tour is best. What matters here is the consequence, which is absolute for anyone buying a joiner seat: the Big Lagoon is on Tour A, the Small Lagoon is on Tour D, and one shared boat runs one route.

So there is no ticket that includes both lagoons on one day. The options are two mornings on two joiner boats, or a private boat that can be sent wherever you like, and even a private A and C boat goes to the Big Lagoon and the Tour C beaches rather than to both lagoons. Two days is the clean answer, and since the ₱400 eco fee is paid once and holds for ten days, the second morning adds only the boat.

What you pay at the mouth

The users fee is ₱200 a person at each lagoon, one-time, paid in cash at the entrance, and it is separate from the ₱400 eco-tourism fee that covers every site in El Nido. The kayak is separate again. Rates quoted for the Big Lagoon inlet run from ₱250 in one visitor guide to ₱350 for a two-seater and ₱500 for a three-seater on one of the tour listings; at the Small Lagoon, one listing prices a two-seater at about ₱300 an hour.

Call the kayak compulsory in practice. Reviewers on the shared Tour A make the point plainly: having paid the lagoon fee, there is no other way in, so the optional line on the listing is optional only in the sense that skipping the lagoon is. The full breakdown of fees, kayaks and cash carries the arithmetic for a whole day.

The tide changes the entrance

Tide is the variable nobody books around and everybody remembers. At high tide the boat anchors close and you paddle straight in through the inlet. At low tide the boat anchors further out, the water over the entrance shallows, and getting in means walking or dragging the kayak over gravel and broken coral. That is the moment reef shoes stop being a suggestion, and they rent for about ₱100 a pair where a listing does not include them.

The Small Lagoon has its own version of the same problem: the gap is low, so a swell or a low tide makes the entry fussier. Neither is dangerous and neither cancels a stop. It just changes a five-minute glide into a twenty-minute scramble, and on a boat with a schedule that comes out of your time inside.

The fleet's clock

Joiner boats report between 8:30 and 9:00 am and leave El Nido town beach between 9:00 and 9:30 once the Coast Guard clearance comes through, which puts most of them at their first stop between 10:00 and 11:00. Operators stagger the order of stops precisely to avoid arriving together, so a boat that starts at Seven Commandos reaches the Big Lagoon later, and a boat that goes to the lagoon first is there in the quietest part of the morning.

You cannot choose that order on a joiner seat, and it is worth asking the office the evening before which way their boat runs. Visitor guides report the earliest allocated Big Lagoon slot at 7:00 am, which no shared boat leaving at 9:00 can reach.

What an early boat buys

A private boat can leave when it likes, and that is the one lever that reliably changes the lagoon experience. A reviewer on the private A and C boat records leaving at 7:00 a.m. and being first at every spot; another writes that the guide reordered the day to hit each sight at its least busy hour. Town operators sell the same trick on private charters as an early or late departure, roughly 8:00 am or 10:45 am instead of 9:00, or the standard route run in reverse.

On a joiner boat the equivalent lever is the route itself. Tour D's lagoon is quiet at any hour, which is the practical reason to consider it when the Big Lagoon is the thing everyone else has come for.

Book Tour A for the Big Lagoon if

The scale is what you came for, you have the stamina for a 90-minute paddle, and you accept a queue at the inlet and a small chance of being sent elsewhere if the day's entries are gone. Tour A also carries the Secret Lagoon, Shimizu Island for lunch and snorkelling and Seven Commandos Beach, so the rest of the day is strong on its own terms, and it is the cheapest route to buy: shared seats start at $22 on the listings compared here.

Bring ₱400 for the eco fee, ₱200 for the lagoon and the kayak share on top, in small notes, because nobody at the inlet takes a card. Ask the operator the evening before which stop the boat runs first: a Tour A boat that opens its day at the lagoon sees a different place from one that arrives after lunch.

Book Tour D for the Small Lagoon if

You would rather have a lagoon to yourself than the biggest one, you are travelling with children or weak swimmers who do better in shallow water, or the Big Lagoon's entry limit worries you. Tour D adds Cadlao Lagoon at no separate fee, sits close to town, and is one of the routes that keeps running when the weather closes the far side of the bay.

One listing shortens the whole transaction: the Tour D that already contains the fees puts the eco fee and the lagoon fee inside the ticket, leaving only the kayak to settle in cash at the water. Families weighing the routes will find the ages, fees and swim notes in island hopping with kids, and the whole line-up sits in every El Nido boat tour compared.

Neither lagoon disappoints. What decides the day is which one you are prepared to share: the Big Lagoon is worth the queue at the inlet and the 90 minutes it asks for, and the Small Lagoon is worth booking precisely because almost nobody makes it the reason for their trip. Two mornings settle the argument for the price of one extra boat and no extra eco fee.

The routes, the fees they leave you to pay in cash and the boats that run them sit in the El Nido island hopping comparison.