Coastal aquaculture has been growing rapidly in the last decades as a response to the global seafood demand and overexploited wild marine populations. As more sustainable food production practices are sought, the attention on the production of low trophic level organisms has increased significantly. Responsible production of primary producers and primary consumers in coastal areas can help meet the ever-increasing seafood demands and ease burdens on natural resources. However, conditions in coastal areas are not easy to control, and changes in ambient factors can impact coastal aquaculture productivity in various ways. Temperature and pH are factors that are already changing globally and are expected to keep changing in response to climate change.

The growth and chemical composition of primary producers, like algae and seaweed, are influenced by the ambient conditions where they grow. Their cells can chemically adapt to the environment, responding to changes in ambient conditions by producing biomass with different nutritional values. Primary producers are the base of the food chain in aquatic ecosystems, serving as a food source for consumers at higher trophic levels. Herbivores and filter feeders directly depend on the availability of good quality primary producers' sources, hence, any changes in the nutrient content and growth of primary producers will affect the ability to produce these species. Therefore, to assure sustainable growth of coastal aquaculture, it is important to understand how species of interest are affected by the changes in ambient conditions predicted due to climate change, and how they interact and relate to each other.

Here, the relationship between environmental conditions, primary producers, and primary consumers was explored. The main goal of this study was to understand how changes in temperature and pH can influence the production of herbivore species in coastal areas, by changing the nutritional value of their diets. For this, as a first approximation, a microalgae culture system that maintained multiple pH cultures through automatic addition of CO2 to keep the desired pH was designed, and the effects of temperature and pH on the growth and protein content of two species of marine microalgae were explored. The species Nannochloropsis oculata and Chaetoceros gracilis were selected for this study as they are important species in coastal aquaculture of filter feeder species. The study consisted of growing these two species under two different temperatures, 13°C and 20°C, and two pH levels, 8.2 and 7.6, representing the current and projected ocean conditions, in Northern California, due to climate change, respectively. The highest final cell count, specific growth rate, and protein content were found when both species of algae were grown at 20°C and pH 7.6, indicating the projected conditions caused by climate change did not have negative effects on the marine microalgae tested. The statistical analysis results for all the parameters suggest that temperature has a bigger influence than pH on both species of algae.

Then, the effects of temperature on the growth and nutritional composition of the marine seaweed Palmaria mollis (dulse) were studied. Dulse is a red seaweed popular in aquaculture, widely used in the production of red abalone in Northern California. The study consisted of growing dulse under three different temperatures, 13°C (current mean ocean temperature in Northern California), 15°C, and 17°C (representing projected temperatures due to climate change). Dulse was grown for 21 days, and its growth, protein, fatty acids, and carbohydrate content were monitored. The results showed that the growth and protein content of dulse were affected by temperature. A negative correlation between temperature and the growth of this species was observed. Dulse grown at 13°C gained the most biomass during the experimental period; however, it contained the least amount of protein in their dry matter. There were no significant differences in the fatty acids and carbohydrate content among the temperatures tested. However, a significant difference in the distribution of fatty acids was found. Dulse growing at 13°C showed the highest percentage of monounsaturated fatty acids and the lowest percentage of saturated fatty acids. The results suggest that changes in temperature predicted due to climate change will affect the nutritional value and the availability of P. mollis, potentially affecting the production of herbivores that depend on them.

Lastly, the influence of rising ocean temperature on the juvenile red abalone (Haliotis rufescens) through changes in its food source was studied. Three different diets were prepared by growing dulse under three different temperatures, 13°C, 15°C, and 17°C. Juvenile red abalone were grown under ambient conditions for 105 days with the prepared dulse as their only food. Abalone growth was measured at Days 0, 40, 75, and 105, and their chemical composition, protein, carbohydrate, and fatty acids, were analyzed at the end of the experiment. Abalone fed dulse growing at 17°C showed higher cumulative growth rates, final condition factor, and specific growth rate. The abalone weight seemed to be more affected by the diets than the shell length. No significant difference was found in their chemical composition across treatments. The results suggest that higher temperatures due to climate change tested in this study do not have negative indirect effects on the juvenile red abalone.

The results of this study suggest that rising ocean temperature and ocean acidification caused by climate change might have positive effects on the protein content and the growth of the marine microalgae studied. Furthermore, temperature seemed to be a more influential factor than pH. In the same way, rising ocean temperature positively affected the protein content of the seaweed studied, however, its growth and condition deteriorated as temperature increased. Therefore, even though dulse growing at 17°C yielded higher growth rates of abalone, keeping this seaweed at higher temperatures will not be sustainable. The different diets used for this study did not affect the nutritional composition of the juvenile red abalone. Finally, higher temperatures due to climate change did not seem to have negative indirect effects on the juvenile red abalone and overall dulse growth rate was the only factor studied that was negatively affected by the predicted conditions due to climate change.

Delta smelt (Hypomesus transpacificus) (DS) are an endangered species of fish in the Osmeridae family. They are endemic to the Sacramento/San Joaquin Delta (Delta). This thesis explores the application of an Egg Frame Box (EFB) created by the Lake Suwa Fishing Collective (LSFC) as a means to hatch DS eggs into the Delta in an effort to reduce hatchery characteristics by investigating the fluid dynamics inside and around the EFB through computational fluid dynamics simulations and found that the water decelerates significantly before entering the EFB and further decelerates upon entering the EFB, to a suitable water flow velocity for DS egg incubation. Studying the effects of water temperatures on the hatching and survival rate of DS eggs adhered to the EFB found that temperature plays a significant role in the fertilization and survival of DS eggs, as well as showing that DS eggs can hatch at the water flow velocity found during simulations. Another study focused on testing how alternative egg frame material for the DS eggs to adhere to affects their hatching and survival rate and found that DS eggs can adhere to and hatch from the substrates tested in a similar rate as the egg frame from the LSFC, demonstrating that locally bought, biodegradable items can be used to as a substitute for the egg frame substrate. Last, we studied the effects of different humidities on DS eggs to evaluate how transporting the eggs outside of water will affect their hatching rate and found that DS eggs are extremely sensitive to being removed from their aquatic environment and should remain submerged throughout their transport to the deployment site. Overall, this thesis provides valuable insight into DS eggs in an effort to restore the wild population from its endangered status in the Delta.