In this study, the long-term effects of different salinities on the performance, sludge morphology and shifts in microbial communities were studied in a simultaneous anammox and denitrification (SAD) process at a C/N ratio of 0.5. Stable nitrogen removal efficiencies of 86.96 and 84.58% and nitrogen removal rates of 0.95 and 0.93 kg (m
3
d)
−1
could be achieved under low (25 mmol l
−1
) and moderate (50 mmol l
−1
) salinity, respectively. However, the performance collapsed when the system was exposed to high salinity (100 mmol l
−1
). The content of extracellular polymeric substances increased as salinity increased, which resulted in larger sizes of granular sludge under low and moderate salinities. Nevertheless, high salinity shock disintegrated granular sludge, thereby decreasing the average granule size. The Illumina-Miseq sequencing results revealed that
Candidatus Jettenia
was the sole salinity-tolerant AnAOB genus during the entire operation, whereas the main denitrification bacterial genera shifted from
Denitrisoma
under low salinity to
Denitrisoma
,
Thauera
and
Ignavibacterium
under high salinity. The results of this study provide a comprehensive and practical evaluation of the SAD process for organic nitrogen-rich saline wastewater treatment.
Effects of salinity on the simultaneous anammox and denitrification process: performance, sludge morphology and shifts in microbial communities