The Plitvice Lakes National Park is inscribed on UNESCO’s World Heritage List. The lake system is composed of 16 cascading lakes of different sizes separated by tufa barriers, which are the park’s key phenomenon. The lakes are characterized by highly diverse trends of the characteristic hydrological indicators—mean annual water levels, discharges, and tufa barrier growth. The analyses carried out in this paper identified that in the period before the early 1990s, Kozjak Lake had a trend of decreasing discharges, together with a trend of increasing water levels and growing tufa barriers. In contrast to this, in the period after 2001, a trend of increasing discharges was recorded, as well as a trend of decreasing water levels and decreasing tufa barriers. A potential cause of the barriers decreasing in size were the extremely high discharges during the last decade, which resulted in increased erosion of the tufa barriers. Losses of water due to the sinking from the lake system as well as the upper Korana course were confirmed, and it was identified that during the analyzed period the losses had not changed significantly. It was determined that the losses of water from Kozjak Lake occurred during low-water periods; however, they depended not only on the quantity of water flowing through the lakes but also on the hydrological conditions underground. The analyses carried out and the methodological procedures used in the analyzed area of the Plitvice Lakes are useful examples for the performance of analyses at similar lakes in karst formed by tufa deposition processes.