Mission Bay (San Diego, California) is located along the Pacific Flyway and is an important habitat for waterbirds in the winter. Little has been documented about this habitat and this project aims to create a baseline to establish an understanding of how waterbirds use Mission Bay, as well as comparing current bird species presence to presence in the past. Mission Bay was divided into grid areas and each was surveyed twice daily at high and low tides. Waterbird activity included foraging, non-foraging, and flying was recorded during each survey over a two-year period from mid-October through January in 2013-2015. Data extracted from this dataset were combined with wetland area, natural area and historic wetland area and was analyzed to understand relationships of independent variables by bird group using a Zero-Inflated Negative Binomial regression model and by waterbird biodiversity using an Ordinary Least Squares regression model. In addition, waterbird habitat was documented across natural and man-made areas. More waterbird species were sighted during contemporary surveys in comparison to historic data from the 1950's and 1970's with similar biodiversity estimates determined for San Diego Bay. Results indicated that geographical area and the presence of wetland habitat significantly affected the biodiversity of waterbirds using Mission Bay in the winter with the highest biodiversity occurring in the largest wetland area in the Kendall-Frost Mission Bay Marsh Preserve. The combination of high biodiversity occurring in the largest wetland area with restricted access to the marsh suggests that human disturbance reduces species richness in this area, confirming the impact of disturbance on sensitive waterbird species cited in other research. Most bird groups favored north Mission Bay with the exception of herons and gulls that preferred southern areas of the bay, likely due to opportunistic interaction with humans, as gulls demonstrated a negative association to natural area size. Favorable conditions occurred mid-winter for Eared Grebe (Podiceps nigricollis) and Pacific Black Brant (Branta bernicla nigricans) as the height of the population appeared early in winter. Presence and activity of shorebirds were associated with tidal cycle with shorebirds foraging at low tide and non-foraging activities at high tide. Cooler water temperature was preferred across several bird groups including Black Brant which may be in response to eelgrass fluctuation. Overall, more bird abundance and biodiversity were present the second year compared to the first. Twenty-two waterbird species out 72 of the total species documented during the project used man-made resources during winter and this may be at an advantage in the future compared to more sensitive species as wetland loss occurs with climate change and the increase in urbanization in natural areas. Increasing wetland area through ongoing restoration and reproduction of wetland habitat of similar quality may maintain or increase species richness with a higher carrying capacity of waterbird numbers present today. However, recreational use of Mission Bay in the winter as warmer temperature is more frequent, is likely to be a threat to waterbirds that use this area due to disturbance. The results of this study suggest that current restoration and expansion of wetland area implement restricted public access to the area.