El Nido Island Hopping Tour A: The Complete Lagoons & Beaches Guide

If you only do one boat trip in Palawan, make it El Nido Island Hopping Tour A. It is the single most popular day on the water in the whole Philippines, and for good reason: in one well-paced day it links the five most photographed stops in Bacuit Bay - the Big Lagoon, the Small Lagoon, the Secret Lagoon, Shimizu Island, and Seven Commandos Beach. This guide covers exactly what you will see, the geology and history behind the scenery, how Tour A differs from B, C, and D, the eco-fees, the conservation rules, the honest weather caveats, and a practical how-to so your day runs smoothly.

What is El Nido Tour A?

El Nido's island-hopping trips are organized into four standardized routes - Tour A, B, C, and D - each visiting a fixed set of islands and lagoons in the Bacuit Archipelago. Tour A is the lagoons-and-beaches route. A typical day starts with a mid-morning departure from the El Nido town beach aboard a traditional outrigger boat, called a bangka, and returns in the late afternoon. Along the way you cover five signature stops.

The five Tour A stops

• Big Lagoon - the showstopper. A wide emerald channel on Miniloc Island, walled by sheer limestone cliffs, that you enter by kayak or paddleboard. On a calm, sunny day the water glows an unreal shade of green.
• Small Lagoon - reached through a narrow gap in the rock that you swim or paddle through into a quiet, cliff-ringed pool. There is often a small cave to peek into at one end.
• Secret Lagoon - a hidden cove you access through a low crack in the limestone wall, opening onto a sheltered patch of sand surrounded by towering rock.
• Shimizu Island - the snorkeling and lunch stop. The crew grills a beach BBQ while you drift over coral gardens alive with reef fish.
• Seven Commandos Beach - a long sweep of soft white sand backed by coconut palms, the relaxed final stop before the ride home.

The geology: why Bacuit Bay looks like this

The jagged towers of El Nido are not volcanic - they are karst limestone, formed from ancient coral reefs and marine sediments laid down over 250 million years ago, in the Permian period. Over geological time, mildly acidic rainwater dissolved the soluble limestone along cracks and fault lines, carving the rock into knife-edged pinnacles, caves, and the very lagoons you paddle through today. The same process built the famous karst landscapes of Ha Long Bay in Vietnam and Krabi in Thailand. The lagoons themselves are essentially flooded sinkholes and collapsed caverns, their entrances the gaps where the rock finally gave way to the sea. It is a living, eroding landscape - and an extraordinarily fragile one.

A short history of El Nido

The town's name comes from the Spanish el nido, meaning "the nest." It refers to the nests of swiftlets - small birds that cement their nests of saliva to the cliff walls and caves of the archipelago. For centuries these edible nests were harvested and traded for use in bird's-nest soup, a prized delicacy in Chinese cuisine, and the trade gave the settlement its identity. For most of its history El Nido was a remote fishing village reachable only by boat or a long, rough overland trip.

That changed from the 1980s onward, when the spectacular bay began drawing divers and adventurers, and El Nido grew into one of Southeast Asia's flagship eco-tourism destinations. Much of Bacuit Bay was placed under protected status as a managed-resource protected area, and over time the local government introduced regulated tour routes, boat-number limits, and visitor fees to balance tourism against conservation. Today El Nido is world-famous, regularly topping "best islands" lists, yet it still wrestles with the same question every popular destination faces: how to share paradise without loving it to death.

Tour A vs B, C, and D - which should you pick?

All four routes are full-day boat trips with lunch, but each visits different parts of the archipelago:

Tour A - Lagoons & Beaches

The classic and most popular: Big Lagoon, Small Lagoon, Secret Lagoon, Shimizu Island, and Seven Commandos Beach. Best for first-timers and anyone who wants the iconic lagoons.

Tour B - Caves & Beaches

Typically Snake Island (a long sandbar), Cudugnon Cave, Pinagbuyutan Island, and Entalula Beach. Quieter than A, with caves and sandbars instead of lagoons.

Tour C - Hidden Beaches & Shrine

Often the favorite of repeat visitors: Helicopter Island, Matinloc Shrine, Secret Beach, Hidden Beach, and Star Beach. More dramatic snorkeling and remote scenery, a longer ride.

Tour D - Lagoons & Beaches (the quieter cousin)

Cadlao Lagoon, Paradise Beach, Pasandigan Cove, Bukal Island, and Natnat Beach. Closer to town, generally the least crowded.

If it is your first visit, do Tour A first, then Tour C if you have a second day. Many travelers combine A and C as the two essential trips.

The Eco-Tourism Development Fee (ETDF)

Every visitor doing island tours in El Nido must pay the Eco-Tourism Development Fee. Under the June 2024 municipal ordinance the standard rate rose to about PHP 400 per person, valid for 10 days, with a higher rate for longer stays and reduced rates for students, seniors, PWDs, and children. You pay it once - at the tourism office or through your tour operator - and the receipt covers all your boat tours within that window, so keep the receipt to avoid paying twice. The fee funds waste management, environmental protection, and sustainable-tourism infrastructure in the bay. It is almost always charged separately from the tour price, so budget for it. Note that some lagoon activities, such as the Big Lagoon kayak, may carry a small separate rental or entrance fee.

Conservation rules to respect

• Use reef-safe (mineral) sunscreen - oxybenzone-based sunscreens damage coral and are discouraged.
• Do not touch or stand on coral when snorkeling; broken coral takes decades to regrow.
• Take all trash back with you - single-use plastics are increasingly restricted.
• Keep a respectful distance from marine life and never feed the fish.
• Boats follow assigned moorings and visitor caps at the lagoons to limit crowding and anchor damage.

Best time to go - the honest weather caveat

El Nido has two broad seasons. The dry season (roughly December to May) brings the calmest seas, clearest water, and the best lagoon colors - this is peak season, with March to May the hottest and busiest. The wet season (June to November) sees more rain and the occasional storm; tours can be cancelled for days when the sea is rough, and water clarity drops after heavy rain. The shoulder months can still be lovely and far less crowded. Be honest with yourself about timing: if your trip falls in the rainy months, build in a buffer day in case the coast guard suspends boat trips for safety. For a fuller breakdown, see our best time to visit guide.

How to do Tour A - a practical how-to

Getting to El Nido

Most travelers fly into either El Nido (Lio) airport or Puerto Princesa and then take a 5-6 hour van transfer north. Weigh the convenience of flying against the cost of the road trip in our ferry vs flight comparison, and plan your overall trip budget with our Philippines travel expenses guide.

Booking

You can book Tour A through a licensed operator online in advance (recommended in peak season, when boat slots sell out) or through a town agency the day before. Either way, confirm that the price includes lunch, snorkel gear, life jackets, and town pickup, and clarify whether the ETDF is extra.

On the day

• Pickup is usually around 8:30-9:00 AM from your hotel in town.
• Bring: reef-safe sunscreen, a hat, rash guard, dry bag, towel, water shoes, and cash for the ETDF, optional kayak, buko, and tips.
• Big Lagoon is busiest late morning - if your boat reaches it early, you will get those mirror-calm photos before the crowds.
• The day wraps up around 4:00 PM back at the town beach.

Is Tour A worth it?

Yes - unequivocally. Tour A packs the defining scenery of Palawan into a single, easy, well-organized day: the cathedral cliffs of the Big Lagoon, the thrill of swimming into a hidden lagoon, snorkeling over living reef, and ending barefoot on a postcard beach. Pay the eco-fee gladly, follow the conservation rules, pick a calm-sea day if you can, and you will understand exactly why Bacuit Bay is regularly ranked among the most beautiful places on Earth. For more itineraries and trip planning, browse our Philippines travel guides.