[9] A small fish, only rarely longer than 5 cm (2 in), the northern tidewater goby is elongate with a blunt tail.

Tidewater gobies, like many fish, exhibit countershading and tend to be mottled slightly darker on the dorsal side.

Breeding individuals will demonstrate color changes, with the males becoming more black with white spots as females become tan or reddish-brown with golden or dark-brown sides.

Juveniles have been found as far upstream as 12 km, e.g. in Ten Mile River, Mendocino County, and San Antonio Creek and the Santa Ynez River, Santa Barbara County, sometimes in sections of stream impounded by California Golden beavers (Castor canadensis subauratus) which provide ideal slow-moving water habitat for northern tidewater gobies.

The northern tidewater goby may be found in small groups of less than a dozen or occasionally in large aggregations of hundreds.

Females will become aggressive during the spring and fight over a potential mate, slapping each other with their tails and biting when posturing is insufficient to drive their rivals away.

In some lagoon populations, gobies have been found to feed on seasonally available invasive New Zealand mud snails, reflecting the fish's adaptive foraging behavior to non-native species in its environment.