Lake Rutajärvi (surface area 1100 hectares) divides the National Park into two parts. Its water level has been lowered twice in the end of the 1800s, 4 metres altogether. Following the water level drop, many small islands were formed in the lake. They are important for landscape and nature conservation reasons. The rocky old shoreline can be seen, for example, along the trail going to Joutsniemi.
Because of the descent in the water level, spruce bogs affected by floods have also developed on the shores. On the old accretion areas grow many rare plant species, such as the Early Marsh-Orchid (Dactylorhiza incarnata) and the Spatula Leaf Sundew (Drosera intermedia). The shores on Syysniemi side of the lake have been state-owned land for a long time, and therefore no summer cottages have been built there. That is why they are virtually in their natural state.
The nesting birds of Lake Rutajärvi include the Black-throated Diver (Gavia arctica), the Whooper Swan (Cygnus cygnus), the Common Sandpiper (Actitis hypoleucos), Great Crested Grebe (Podiceps cristatus) and Red-necked Grebe (Podiceps grisegena). The Goldeneye (Bucephala clangula) nests on small peaceful lakes.
Lake Rutajärvi and Lake Päijänne are connected by Rutajoki River with many rapids. Lake Päijänne is 45 metres lower, so at some places the rapids are steep and waterfall-like. The rapids also make the water rich in oxygen, and therefore Rutajoki River is an important breeding area for the Brown Trout (Salmo trutta lacustris), which needs oxygenous water. Rutajoki River has been cleared and a dam built in the upper course. However, the surroundings have stayed almost in their natural state.