Emissions from thousands of in-use heavy-duty diesel trucks were sampled at a highway and an arterial street location in the San Francisco Bay Area, spanning a time period when use of diesel particle filters (DPFs) and selective catalytic reduction (SCR) increased rapidly. At the highway site where a diverse mix of trucks is observed, SCR systems on 2010 and newer engines reduce emitted nitrogen oxides (NOx) by 87 ± 5% relative to pre-2004 engines. SCR also mitigates DPF-related increases in nitrogen dioxide (NO2) emissions. However, a majority of trucks had in-use NOx emission rates that exceeded applicable emission standards. SCR systems increase emissions of nitrous oxide (N2O) and ammonia (NH3) from near-zero levels to 0.93 ± 0.13 and 0.18 ± 0.07 g kg–1, respectively. Emissions of all nitrogenous species and especially NH3 are skewed; 10% of trucks contribute 95% of the on-road fleet’s total NH3 emissions. Similar emission changes are observed at the arterial street site where exclusively drayage trucks operate. The environmental effects of decreased black carbon, NOx, and carbon dioxide (CO2) emissions and increased N2O and NH3 emissions due to the rapid adoption of DPF and SCR systems by the California truck fleet are: (1) a 65% net decrease in the social cost of statewide exposure to diesel truck emissions (−3.3 billion 2018 US dollars per year), and (2) a 3% net decrease in the global warming potential-weighted emission factor (−27 g CO2-eq km–1).