Inequality　in　water　allocation　and　the　shortage　of　water　resources　are　two　of　the　main　critical　components　of　multi-regional　water　system　management.　The　impact　of　virtual　water　flows　implied　in　inter-regional　trade　on　multi-regional　water　resources　issues　is　often　ignored,　especially　on　issues　as　complicated　as　water　quality-based　and　water　quantity-based　issues.　Therefore,　a　multi-region　blue/grey　water　management　system　is　developed　in　this　study　with　a　detailed　case　study　of　the　Yangtze　River　Economic　Belt　(YREB).　In　detail,　both　blue　water　footprint　(BWF)　and　grey　water　footprint　(GWF)　are　considered　in　the　proposed　model.　And　the　virtual　water　flows　inherent　in　inter-provincial　trade　are　quantified　using　a　multi-regional　input-output　analysis.　Based　on　this,　the　blue　water　and　grey　water　metabolic　systems　are　next　assessed　respectively　in　terms　of　system　health　state,　regional　resource　inequality,　and　the　water　scarcity.　In　particular,　the　impact　of　virtual　water　transfers　is　also　innovatively　examined　in　this　context.　It　shows　that　water　pollution　affects　most　of　the　YREB　provinces　(Shanghai　(SH),　Jiangsu　(JS),　Anhui,　Hubei,　Yunnan,　Jiangxi).　And　SH　and　JS　suffer　from　shortages　of　available　water,　with　the　water　availability　scarcity　index　for　both　provinces　being　above　0.4　during　the　study　period.　The　transfer　of　virtual　blue　water　(BW)　exacerbates　overall　BW　inequalities　while　alleviating　water　availability　shortages　in　most　provinces　(except　SH,　Zhejiang,　Chongqing,　Sichuan).　Differently,　the　transfer　of　virtual　grey　water　(GW)　has　a　mitigating　effect　on　overall　GW　inequalities.　And　it　has　the　highest　impact　on　SH＇s　water　quality　shortage,　with　a　virtual　grey　water　transfer　impact　coefficient　of　23.64　in　2007.　The　findings　provide　a　new　pathway　for　coordinated　water　management　intra-and　inter-provinces,　as　well　as　a　reference　for　the　development　of　multi-regional　water　management　policies.