The Port of Bay City has a humid subtropical climate with hot humid summers and mild winters. Temperatures in the Port of Bay City range from an average high of 29°C (84°F) in July and August to an average low of 13°C (55°F) in January. Rain is greatest in the Port of Bay City in September and October and in May and June, peaking in September at almost 14 centimeters (5.75 inches). Humidity levels in the Port of Bay City range from 70% in December and January to about 62% in October. The Port of Bay City gets negligible snowfall.

The most popular tourist destination in the Port of Bay City is the Matagorda County Birding Nature Center (MCBNC). Located on the riverfront, the MCBNC has a put-in/take-out point for paddle boats including kayaks, canoes, and rafts. The MCBNC features three major eco-systems and seven botanical gardens. The Cactus Garden contains varieties of cacti from around the world. The Butterfly Garden, containing the Julia Hill Memorial Sun Dial, has many flowers that butterflies love and a grape arbor at its entrance. The Hummingbird Garden was designed to attract hummingbirds and butterflies. The Rose Garden features antique roses dating back to the 18th Century, although it also has new rose varieties, climbing roses, and an arbor. The Herb Garden is a fragrant four-quadrant circle that contains one-half herbs and one-half native Texas plants. The Palm and Bambo Garden contains Texas' only native palm, the Texas Sabal, and several varieties of palms from around the world.

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