The Ports of Los Angeles and Long Beach, collectively known as the San Pedro Bay Ports, serve as vital gateways for freight movement in the United States. The COVID-19 pandemic and other influencing factors disrupted freight movement and led to unprecedented cargo surge, vessel congestion, and increased air pollution and greenhouse gas emissions from seaport and connected freight system operations beginning in June 2020. In this study, we conducted the first comprehensive monthly assessment of the excess particulate matter, oxides of nitrogen (NOx), and carbon dioxide (CO2) emissions due to the heightened congestion and freight transport activity from ocean-going vessels (OGVs), trucks, locomotives, and cargo handling equipment (CHE) supporting seaport operations. Excess emissions peaked in October 2021 at 23 tons of NOx per day and 2001 tons of CO2 per day. The strategic queuing system implemented in November 2021 significantly reduced the number of anchored and loitering OGVs and their emissions near the ports, even during continued high cargo throughput until Summer 2022. Looking forward, we analyzed projected emissions benefits of adopted California Air Resources Board regulations requiring cleaner and zero-emission trucks, locomotives, and CHE over the next decade. If a repeated port congestion event were to occur in 2035, NOx emissions from land-based freight transport should be lessened by more than 80%. Our study underscores the potential emissions impacts of disruptions to the freight transport network and the critical need to continue reducing its emissions in California and beyond.