The preserve is a patchwork of natural and modified landscapes. The Palo Alto Flood Basin, bordered by Adobe Creek and Matadero Creek, sits a couple of feet below sea level, deliberately maintained as a catchment basin to protect lower Palo Alto from flooding. In the late 1920s, levees were constructed to reroute San Francisquito Creek away from its former mouth, creating a sharp northward turn before the creek exits to the Bay. Dredging from the former Yacht Club site produced landfill that was used to build the Palo Alto Airport and the Municipal Golf Course, and by 2004 these filled areas had reduced the preserve's tidal marsh to just 352 acres. Fifteen miles of multi-use trails wind through this mixture of tidal and freshwater habitats, connecting the Duck Pond, the Baylands Athletic Center, the Sailing Station, and the Harriet Mundy Marsh.

The preserve's interpretive center bears the name of Lucy Evans, a Stanford graduate of the class of 1929 who taught at Mayfield School for 23 years. Evans fought tenaciously for the preservation of the Baylands at a time when wetlands were routinely dismissed as wasteland ripe for development. Her determination earned her the nickname Baylands Lucy among those who knew her. She died suddenly in 1978, and the Baylands Nature Interpretive Center was rededicated in her memory that December. Built on pilings at the edge of the salt marsh, the center sends a plank boardwalk a quarter-mile across the marsh to open water, where visitors are rewarded with a panoramic view of San Francisco Bay. The interpretive center was renovated in 2017 and the boardwalk in 2019.

Beneath the surface, the Baylands preserve harbors a surprisingly active aquatic ecosystem. Adobe Creek carries approximately 5.5 miles of perennial flow above Manresa Way in Los Altos, with habitat suitable for trout spawning and rearing. Matadero Creek provides 3.9 miles of perennial flow above Bol Park in Palo Alto, plus 1.4 miles along its Deer Creek tributary. Within the Flood Basin itself, 2.5 miles of Adobe Creek and 1.8 miles of Matadero Creek provide stretches where young steelhead can safely grow to a larger size before making the journey to the Bay and ultimately the Pacific Ocean. That steelhead still navigate these creeks in the shadow of Silicon Valley is one of the Bay Area's more remarkable ecological stories.

The Byxbee Park Hills area, named for John Fletcher Byxbee Jr., Palo Alto's city engineer from 1906 to 1941, offers elevated views across the preserve. Byxbee was a member of the first graduating class of Palo Alto High School and studied engineering at Stanford under C. D. Marx, the founder of Palo Alto's utilities system. From the park's hilltops, the salt marsh stretches to the Bay in bands of green and brown, punctuated by the white shapes of egrets and herons. On clear days, the East Bay hills form a distant backdrop. It is a landscape that rewards patience and quiet attention, a place where the rhythms of the tides still matter more than the rhythms of quarterly earnings reports.