Because of its extreme vulnerability karst aquifer is a challenge in terms of protection, monitoring, maintenance of water quality and exploitation. Hydrologic and hydrogeological processes in karst are extremely unpredictable because of anisotropy and heterogeneity of the aquifer. Assessment of regional hydrodynamics of underground karst terrain is often extremely difficult task. Each karst aquifer has specific hydrogeological and hydrologic properties, which ultimately require a regional measurement and incorporation of gathered data in further modelling and management. The development of new technology based measurement and monitoring of aquifers in the fields of hydro acoustics, radar measurement, sensors and computer technology creates a need to implement theexisting and generate the new protocols and methods of measurement. Furthermore, the new technology provides far greater opportunities and thus they open up new insights related to karst aquifer and revise the old ones. Temporal and spatial resolution of measurements increase whereas computer technology offers an excellent tool for analyzing and establishing a models of processes in nature that lead to a better understanding. The main motivation for this dissertation is the gaining of new knowledge in the dynamics of water within the karstaquifer and on the karst surface, as well as improvement and validation of old findings by studying the dynamics of underground water in the caves and in the case of surface karst lakesand open streams taking into account. Experimental approach and measurement of hydrological episodes within a highly heterogeneous system result with a new insight in the nature of water movement in the karst terrain. The continuous hydrological measurements in a deep karst cave and established models of the measured parameters are presented in this work. Furthermore, the probabilistic concept of discharge measurement in open water course with irregular profile was carried out which led to introduction of new measurement protocols. For the first time, the detailed morphometric measurements using available emerging technologies were conducted for Red Lake and Blue Lake near Imotski. Continuous hydrological measurements of Blue Lake resulted with a hydrological model which is also presented in this work.