Two pilot-scale hybrid moving bed biofilm reactor-membrane bioreactors were operated in parallel for the treatment of salinity-amended urban wastewater under 6 hours of hydraulic retention time and 2500 mg L−1 total solids concentration. Two salinity conditions were tested: the constant salinity of 6.5 mS cm−1 electric conductivity (3.6 g L−1 NaCl) and the tidal-like variable salinity with maximum 6.5 mS cm−1 electric conductivity. An investigation was developed on the biofouling produced on the ultrafiltration membrane surface evaluating its bacterial community structure and its potential function in the fouling processes. The results showed that biofouling was clearly affected by salinity scenarios in terms of α-diversity and β-diversity and bacterial community structure, which confirms lower bacterial diversity under variable salinity conditions with Rhodanobacter and Dyella as dominant phylotypes. Microorganisms identified as bio-mineral formers belonged to genera Bacillus, Citrobacter, and Brevibacterium. These findings will be of help for the prevention and control of biofouling in saline wastewater treatment systems.