On the other hand, the catches of many species have been significantly reduced by the disturbance of native species, caused by the invasion of introduced fish such as the largemouth bass and bluegill, the amendment of the Ordinance on Control of Water Level (琵琶湖水位操作規則の改訂) in 1992, the loss of lagoons and the disconnection of the lake from the network of paddy fields.
その一方で、オオクチバスやブルーギルをはじめとする外来種の侵入や1992年の琵琶湖水位操作規則の改訂、内湖の消失、水田とのネットワークの分断等によって固有の生物相が大きく攪乱を受け、漁獲高が激減した種も多い。