A few weekends ago, I went down to kayak in Elkhorn Slough. I've probably kayaked this area about half a dozen times in total since moving to the bay area, but very few people seem to know about this gem.
The most unique thing about the Elkhorn Slough is probably it's concentration of endangered sea otters. Roughly 5% of California's population of sea otters live in this relatively small slough. Nearby Monterey Bay Aquarium, which does lots of work to protect these sea otters, will release rescued otters into the slough and monitor the population here closely. Simply visiting the harbor area with some binoculars will virtually guarantee sightings of several otters any time of the year.
In addition to otters, the slough is home to a number of other wildlife species, some permanent and others migratory. I generally see my fill of seals and sea lions, as well as several large birds such as pelicans. Occasionally you'll see some blooms of large jellyfish in the water.
Visiting is easy and you can see a good deal by foot, but I'd recommend exploring in a kayak. There are two kayaking outfitters in the moss landing harbor, and I've gone out with both depending on the day:
Kayak Connection: $35/single, $55/double kayak. Has a small parking lot for customers use. Has dock access for the kayaks, which makes getting in and out a little more finicky, but also doesn't require wading into the water from the shore.
Monterey Bay Kayaks: $30/single, $60/double kayak. Must pay for parking in the moss landing harbor. You launch your own kayak directly from the shore.
I've never bothered with a tour or anything, just a kayak rental for a few hours. The slough is long and narrow making it both impossible to get lost in and also impossible to miss anything. The protected waters are very calm, so the brief kayak training offered as part of your rental is more than sufficient for a complete beginner. They will also outfit you with life vest, spray skirts and jackets, etc. Wear comfortable clothes that can get a little wet, but no special clothing is needed.
I've also never bothered with reservations except for a large group. Only once have I shown up and one of the two outfitters was out of kayaks for the day, but the other still had plenty.
The outfitters will walk you through all of the logistics when you arrive: where to paddle, when to return, how far to go, best places to look for wildlife. However, if you want a preview, here's a map of the slough:
The kayak outfitters are located on the northeast shore of the harbor which is on the west side of this map, near hwy 1. To make navigation easy, just plug one of the two outfitter's addresses into a GPS. The north and south parts of the harbor only connect via Hwy 1 which is a pain to enter, so don't get off onto the south harbor at Moss Landing road, just turn directly into the north harbor area, where you'll see signs for Kayak Connection, the Yacht Club, and some shop selling pots. If you want a place to eat however, the south harbor has several restaurants.
The slough itself can be kayaked about 6 miles each way if you have the time and inclination, though you must return the same route. Rough mile markers are pretty clear (a bouy around mile 1, a dairy around mile 2, etc) and will be pointed out by your outfitter. For a more relaxed adventure though, most of the wildlife hangs out pretty close to the ocean, so you need not go more than a mile to see what you came for.
If you have the luxury of selecting your date and time, you may want to select a time when the tide is going out. This way you'll end up working a bit harder as you enter the slough, but can float on out when you tire and want to return. Also, sometimes the afternoon will present light winds working against you when returning, so having the tide working for you will help. If you give one of the outfitters a call, they can tell you about the tides and winds for the day you'd like to go out and give you relevant advice.