The　current　ecological　compensation　mechanisms　can　promote　cooperation　between　upstream　and　downstream　regions　along　a　river　by　internalizing　the　negative　externalities　of　water　pollution　caused　by　the　upstream　region.　But　the　positive　externalities　of　water　pollutants　elimination　by　those　regions　with　low　pollutant　emission　may　also　result　in　motivations　for　free-riding　in　some　regions　and　hinder　the　cooperation　on　water　pollution　governance.　The　study　theoretically　analyses　the　internal　mechanism　and　influence　of　this　“free-riding　motivation”　under　the　circumstance　of　three　regions　of　which　one　upstream　discharges　pollutants　into　the　river　and　the　others　downstream　in　sequence　need　to　decontaminate　the　pollutants　to　get　clean　water.　When　the　upstream　region　chooses　to　discharge　pollutants　up　to　the　standard　to　avoid　paying　ecological　compensation　to　the　region　in　the　middle　reaches,　the　most　downstream　region　has　a　motivation　for　“free-riding”.　When　the　upstream　region　chooses　to　discharge　excessive　pollutants,　the　downstream　region　will　participate　in　the　water　pollution　governance　cooperation　only　when　the　ecological　compensation　shared　from　the　upstream　region　exceeds　the　cost　of　water　pollution　control　it　shares,　which　will　lead　to　an　unfair　cost-benefit　distribution　and　cause　difficulties　in　negotiation.　The　secondary　pollution　caused　by　the　region　in　the　middle　reaches　may　alleviate　this　problem　to　some　extent.　By　paying　a　certain　amount　of　funds　in　advance　as　a　river　basin　collaborative　governance　fund,　the　downstream　region　will　be　more　motivated　to　participate　in　water　pollution　governance　cooperation.　©　2023　Systems　Engineering　Society　of　China.　All　rights　reserved.