This study presents an integrated assessment of anchorage-related emissions and air quality impacts in the Panama Canal region through Automatic Identification System (AIS) data, bottom-up emission estimation, and atmospheric dispersion modeling. One year of terrestrial AIS observations (July 2024–June 2025) captured 4641 vessels with highly variable waiting times: mean 15.0 h, median 4.9 h, with maximum episodes exceeding 1000 h. Annual emissions totaled 1,390,000 tons of CO₂, 20,500 tons of NO_x, 4250 tons of SO₂, 656 tons of PM₁₀, and 603 tons of PM_2.5, with anchorage activities contributing 497,000 tons of CO₂, 7010 tons of NO_x, 1520 tons of SO₂, 232 tons of PM₁₀, and 214 tons of PM_2.5. Despite the main engines being shut down during anchorage, these activities consistently accounted for 34–36% of the total emissions across all pollutants. High-resolution emission mapping revealed hotspots concentrated in anchorage zones, port berths, and canal approaches. Dispersion simulations revealed strong meteorological control: northwesterly flows transported emissions offshore, sea–land breezes produced afternoon fumigation peaks affecting Panama City, and southerly winds generated widespread onshore impacts. These findings demonstrate that anchorage operations constitute a major source of shipping-related pollution, highlighting the need for operational efficiency improvements and meteorologically informed mitigation strategies.