A more recent concern has developed as the first cruise ship to enter Monterey Bay since 1966 caused environmental groups to demand increased protection for marine sanctuaries and to increase regulation of the cruise ship industry. The water around Monterey Bay has also been affected by sewage spills at local beaches, leading to viral and bacterial contamination. In 2000, four Monterey County beaches were closed because of sewage spills, and twenty-five warning advisories were issued. In 2001, there was one beach closure and eleven advisories. It has also been found that there is inadequate storm pipe maintenance in cities on the Monterey peninsula.

The California Ground Squirrel is a large animal about 383-500mm (18 inches) long, including the moderately bushy tail. The tail is longer than half the head and body length. The squirrel has a general gray-brown coloration mottled or dappled with lighter flecks on its back, and a mantle or darker gray band of color extends from the head down and over the middle of the back. The squirrel's shoulders and the sides of the head are light gray, and there are rarely any stripes. This squirrel is distinguished from other ground squirrels in California by its large size, dark mantle, and usual lack of stripes. The habitat for the California Ground Squirrel covers many plant communities in all the life zones from the coast into the mountains, from southern California to central Washington. Nine ground squirrels are native to California, and it is known that when different squirrels live in the same area, their eating preferences will vary enough to prevent active competition for the same resources. The California Ground Squirrel lives in open spaces and can commonly be found along roadsides, in fields of stubble, or I well-grazed pastures. They are found in the western half of southern California and northwestern Baja California, normally below about 7200 ft. In elevation.

Some damage has been noted for Monterey Bay's kelp forests. These forests consist of giant kelp that can soar 100 feet or more from the ocean floor and that provides habitats ranging from tiny, seafloor caves to dense golden-green canopies just below the water's surface. At each level, creatures big and small find their own niche, such as brittle stars and sculpins within the kelp's holdfast, a root-like structure that anchors the plant to rocks and boulders. In the filtered sunlight of the mid-water region, turban snails and crabs graze on the kelp's thick stipe and are, in turn, grazed upon by lingcod and schools of rockfish. Sea otters swim amid the kelp's upper fronds. These forests require a unique set of conditions to thrive, including hard, rocky seafloors, high concentrations of nutrients, moderate waves, and clear, clean ocean water. The Monterey Bay National Marine Sanctuary spans 350 miles along the central California coast and stands as one of just a few regions in the world that provides the conditions necessary to support kelp forests. Even though this is a protected area, the sanctuary today faces a number of persistent challenges, such as undersea noise from military and commercial operations and even small motorized craft like Jet Skis. These can disrupt marine mammal communication. The area is also subject to pollution from sewage leaks, spills, rain runoff, and the dredging of nearby harbors. The human threats are clearly numerous. The nature of the pollution threat is evident from a 1966 analysis of coliform bacteria off Del Monte Beach:

Determination of the distribution of coliform bacteria in the vicinity of the outfall effluent of the Monterey Water Pollution Control Plant was made using the membrane filter technique for enumeration. The coliforms were seen to follow the onshore mass transport of water in the surface layer in response to predominately westerly winds. The extent of penetration of coliforms into the bay north of the outfall is restricted to several hundred yards, while more extensive spreading was observed towards the surf zone. No consistent pattern of variation of the coliform distribution would be related to the tidal cycle. Higher concentrations of coliform bacteria on several occasions seemed to be related to reduced periods of solar radiation.

The problem has increased since that time as the population has also increased in the area.

Intermittent problems occur from time to time and threaten the ecology of the region as well. One such incident was in 1997 when a substance in the bay disabled some 400 birds. The problem dissipated on its own in a few days and was tentatively identified as a hydrogenated vegetable oil. The source of this substance was not known. It affected the feathers of near-shore birds and made it impossible for the birds to fly. Birds also depend on their feathers for insulation, so oiled birds are vulnerable to food is scarce, and most use stored fat for energy during estivation (during the summer or dry season when the animal is in a torpid state) and hibernation (during the winter when the animal is in a resting state). Ground squirrels usually breed soon after emerging from hibernation and make their nests in the ground or in rock piles. The California Ground Squirrel has a gestation of a month, usually with one litter per year and an average of seven young per litter. The diet for these animals includes a broad range of seeds, berries and leaves of grasses, forbs, and wood plants, as well as bulbs, tubers, insects, and road-killed carrion. They have internal cheek pouches and use thee for transporting food to their burrows. In areas where the number of squirrels is high, their activities, burrows, and food preferences may cause problems for ranchers and farmers. Predators can control squirrel numbers and include coyotes, foxes, wildcats, badgers, large hawks, the golden eagle, and gopher snakes.

Several problems have been cited concerning these animals. Many species of ground squirrels carry fleas, and the fleas can transmit a bacterium responsible for plague. In wild rodents, this plague is called sylvatic plague, and when it is transmitted to humans by the fleas, it causes bubonic plague and pneumonic plague. Campgrounds warn when ground squirrels have tested positive for plague. Health officials dust the openings of burrows with flea powder to reduce the flea population, and prudent behavior calls for leaving the squirrels and other wild animals alone.

The California Ground Squirrel can actually be an indicator of problems because of its being a host for the etiologic agents and vectors of many diseases. These animals serve as subjects for research into the prevalence of certain ectoparasites. The widespread distribution of California ground squirrels is considered significant because their burrows also serve as habitat for California tiger salamanders and California red-legged frogs, and both the California Ground Squirrel and the red-legged frog require animal burrows, principally ground squirrel burrows, in upland areas away from the aquatic environment of streams. Protecting this environment also helps protect the populations of these animals. Observations in Kings Canyon National Park show that there is a prevalence of the California Ground Squirrel and Belding's ground squirrel as well as four species of chipmunks. The greatest threat to these animals is considered to be water pollution, air pollution, loss of natural fire regime, and habitat fragmentation. The most serious air pollution is ozone, which is produced when pollutants from industry and automobiles are heated by sunlight. In 2001, the park recorded more days with unhealthy levels of ozone than any other national park, standing at 61 days. Ozone harms vegetation as well, and the pine trees in the area are especially susceptible so that 90% of the pines in the Giant Forest are show some ozone damage. While Sequoia trees are more resistant, some believe that ozone affects the survival of seedlings. Acid deposition is not yet a problem but could become one as the population in the region increases. Nitrogen deposition is already increasing, probably because of motor vehicles, industry, and agriculture. More nitrogen is being retained in the vegetation in the park. Another threat is from agricultural chemicals such as organo-phosphates and PCBs, which become suspended in the air as particulates and are then deposited in the park. Some scientists believe this harms the wildlife in the park. Pollution has also been contributing to a reduction in visibility. An additional problem caused by human action has been an increase in exotic flora and fauna, and some exotic plants not native to the region have been taking over local…