Ocean　acidification　(OA)　in　estuaries　is　becoming　a　global　concern,　and　may　affect　microbial　characteristics　in　estuarine　sediments.　Bacterial　communities　in　response　to　acidification　in　this　habitat　have　been　well　discussed;　however,　knowledge　about　how　fungal　communities　respond　to　OA　remains　poorly　understood.　Here,　we　explored　the　effects　of　acidification　on　bacterial　and　fungal　activities,　structures　and　functions　in　estuarine　sediments　during　a　50-day　incubation　experiment.　Under　acidified　conditions,　activities　of　three　extracellular　enzymes　related　to　nutrient　cycling　were　inhibited　and　basal　respiration　rates　were　decreased.　Acidification　significantly　altered　bacterial　communities　and　their　interactions,　while　weak　alkalization　had　a　minor　impact　on　fungal　communities.　We　distinguished　pH-sensitive/tolerant　bacteria　and　fungi　in　estuarine　sediments,　and　found　that　only　pH-sensitive/tolerant　bacteria　had　strong　correlations　with　sediment　basal　respiration　activity.　FUNGuild　analysis　indicated　that　animal　pathogen　abundances　in　sediment　were　greatly　increased　by　acidification,　while　plant　pathogens　were　unaffected.　High-throughput　quantitative　PCR-based　SmartChip　analysis　suggested　that　the　nutrient　cycling-related　multifunctionality　of　sediments　was　reduced　under　acidified　conditions.　Most　functional　genes　associated　with　nutrient　cycling　were　identified　in　bacterial　communities　and　their　relative　abundances　were　decreased　by　acidification.　These　new　findings　highlight　that　acidification　in　estuarine　regions　affects　bacterial　and　fungal　communities　differently,　increases　potential　pathogens　and　disrupts　bacteria-mediated　nutrient　cycling.