PAIS hosts a variety of pristine beach, dune, and tidal flat environments,[2] including the Laguna Madre on its west coast, a famous spot for windsurfing.

The island is located along Texas's southern coast of the Gulf of Mexico and is noted for its white sandy beaches.

Padre Island is a very young geological feature that only developed merely 4,500 to 5,000 years ago, according to radio carbon dating of shells.

Constant bombardment of prevailing southeasterly winds from the Gulf of Mexico heap beach of sand into high foredunes.

Active sand dunes march across the island, smothering vegetation in their paths and leaving barren sandflats in their wakes.

In other places, vegetation may win a battle of its own and stabilize the blowing sand by binding it with roots and vines.

Slower daily movements of the sand and stabilizing effects of vegetation are interrupted occasionally by the brutal force of hurricane winds, waves, and tides.

The combination of a high rate of evaporation under the hot Texas sun and little mixing with either freshwater or normal seawater has made Laguna Madre extremely salty.

The lagoon is widest during highest wind tides, which produce maximum flooding of the vast tidal flats.

Within the national seashore, the northern part of the lagoon is occupied largely by grassflats having an average water depth of about 3 feet.

These grassflats are environments of very high biologic activity, serving as spawning grounds for a number of fish, clams, and snails.

The deepest parts of the lagoon are south of the Land-Cut Area, where the muddy sand bottoms lie at depths as great as 8 feet.

A program to re-establish a nesting beach for Kemp's ridley sea turtles on Padre Island was begun in 1978.

It is home to a wide variety of birds when wet, including black-necked stilts, roseate spoonbills, great egrets, American white ibis, and many others.

These items can range from tiny pieces of plastic, hypodermic needles, and lumber, to nets or bleach bottles tossed overboard by shrimpers and even objects as large as buoys and steel containers.

In 2007, Sandifer established the Friends of Padre, a non-profit association to fund park projects and to organize the cleanup.