The Royal National City Park contains many lakes as well as several watercourses. Many of these lakes were previously bays which were transformed into lakes by the land-rise. For example, Brunnsviken in Solna was once the greatest lake in the area surrounded by forested hill slopes and idyllic meadows and pastures. It was this pastoral landscape mirrored in the waters of Brunnsviken that Gustav III, together with his architects and favourites chose as the central focus of their three English landscape parks: Bellevue, Haga and Tivoli. In 1863 Ålkiste Canal was detonated to improve the outlet to Lilla Värtan and the Baltic Sea. This caused the water level to drop by 1.25 metres and Brunnsviken became an inlet once more.
Laduviken on Norra Djurgården is an example of a cut-off sea inlet which became a lake. To the east and west it is bordered by wet woodland. Around the lake there are pleasant walks with picnic sites where barbequing is allowed. South of Laduviken lies the Fiskartorpet open-air recreational centre.
Isbladskärret lies on Södra Djurgården, south of Djurgårdsbrunn Canal which also was originally a sea inlet, Isbladsviken. Damming for that canal lowered its level sharply. When the Royal Djurgården Administration stopped pumping out the marsh in the 1980s, it became an excellent bird lake for species such as mute swan, gadwall, little grebe and heron.
The only watercourse with running water all year round is Igelbäcken, which runs between the lake of Säbysjön on Järvafältet and Edsviken. Its waters are relatively clear and it harbours quite a number of molluscs as well as the stone loach, which is a rare fish. The dipper can be found overwintering here.