Places to Swim Near Shore

The Monterey Bay has 31.5 miles of continuous sandy beach, broken only briefly by the Moss Landing harbor entrance near the center of the bay. Although great for bird watching, quiet walks and collecting sea glass, most of this area is known better for its surf and wildlife than open water swimming.
For more friendly waters and the company of other swimmers, head north or south to the protected water at each end of the bay.
(Scroll down for more info on each area.)
Santa Cruz (West Side)
The most popular open water swimming beach in Santa Cruz is Cowell Beach, located on the west side of the Santa Cruz Municipal Wharf. This small cove is generally protected from the wind by tall cliffs and the setting is idyllic. The small bay is framed by iconic Santa Cruz landmarks, including the Lighthouse Museum, Steamer Lane, The Boardwalk, Surfer Statue, Municipal Wharf, Downtown, and the Santa Cruz Mountains. If you'd like to stay the night, the Dream Inn is located directly on the beach just steps from your morning dip. During the Summer, swim buoys mark an out and back swim that's slightly under 1 mile. Swim to the outer (3rd) buoy and then to the end of the wharf and back to the beach to round up to a mile.  Many others prefer a trip around the 1/2 mile long municipal wharf (shown below). Watch out for fishing lines and curious sea lions.
Just to the east of the Santa Cruz Wharf is
Main beach and the Santa Cruz Beach Boardwalk (shown below). Listen for the screams of thrill seekers as you pass the Giant Dipper roller coaster, following the shoreline to the San Lorenzo River mouth and then to Seabright beach. After approximately 1 mile (one way), you'll reach the Santa Cruz small craft harbor. It's not advisable to swim across the harbor entrance.
From the Harbor beach (east side of the harbor) one half mile of swimming (one way) will take you along Twin Lakes beach to Black Point. Turn around and return to the harbor for a one mile swim. During the summer months, swim buoys stretch from Main Beach to Black Point. 

The area between Black Point and Capitola to the South East is better known for surfing and all around beach going. To continue your swimming tour south, make your way down to Capitola.
Capitola (East Side)
Steps from boutique shops, art galleries, and beach front eateries, the (generally flat) water surrounding the Capitola Wharf (shown below) is a favorite open water playground to locals and tourists alike. A small string of swim buoys makes an ideal course for swimming short laps (300 yards) with the added bonus of lifeguards (in Summer only). To the west of the wharf is a smaller beach (Hoopers) and a protected cove. One circle around the cove is about a quarter mile. Adventurous swimmers head north east from the Capitola Wharf to New Brighton State Beach (1 mile each way). Don't go alone, and be aware on higher tides there is no landing between Capitola and New Brighton.
New Brighton & Seacliff State Beaches
The 1.5 mile stretch between New Brighton (shown below) and Seacliff offers excellent swimming parallel to the beach.

From New Brighton, it's a 2 mile round trip to the Capitola Wharf, or 3 miles down to the boat and back. A round trip from Capitola to the Cement Boat in Seacliff makes for a nice 5 mile outing.
Seacliff State Beach is home to the SS Palo Alto, a cement ship that was towed to Aptos and used for recreation in the late 1920s. The boat remains today as a popular fishing destination and serves as an artificial reef for local wildlife.
Monterey & Del Monte Beaches
Just north of the Monterey Harbor begins a long stretch of beach that runs uninterrupted for over 16 miles on the way to Moss Landing harbor. The first few miles include Monterey Municipal Beach and Del Monte Beach.

Nearby in Pacific Grove, you'll find the clear waters of Lovers Beach, protected from the wind by thick kelp beds and Lovers Point.  This is a picturesque place to swim and the Kelp Krawlers swim group meets here regularly for swims year round. The water here is typically more clear than swim locations on the northern end of the bay, but the water temperature is also slightly cooler. Take a dip then visit the Monterey Bay Aquarium or Cannery Row.