Karst aquifers are characterized by extreme heterogeneity due to the presence of karst conduits embedded in a fractured matrix having a much lower hydraulic conductivity. The resulting contrast in the physical properties of the system implies that the system reacts very rapidly to some changes in the boundary conditions and that numerical models are extremely sensitive to small modifications in properties or positions of the conduits. Furthermore, one major issue in all those models is that the location and size of the conduits is generally unknown. For all those reasons, estimating karst network geometry and their properties by solving an inverse problem is a particularly difficult problem. In this paper, two numerical experiments are described. In the first one, 18,000 flow and transport simulations have been computed and used in a systematic manner to assess statistically if one can retrieve the parameters of a model (geometry and radius of the conduits, hydraulic conductivity of the conduits) from head and tracer data. When two tracer test data sets are available, the solution of the inverse problems indicate with high certainty that there are indeed two conduits and not more. The radius of the conduits are usually well identified but not the properties of the matrix. If more conduits are present in the system, but only two tracer test data sets are available, the inverse problem is still able to identify the true solution as the most probable but it also indicates that the data are insufficient to conclude with high certainty. In the second experiment, a more complex model (including non linear flow equations in conduits) is considered. In this example, gradient-based optimization techniques are proved to be efficient for estimating the radius of the conduits and the hydraulic conductivity of the matrix in a promising and efficient manner. These results suggest that, despite the numerical difficulties, inverse methods should be used to constrain numerical models of karstic systems using flow and transport data. They also suggest that a pragmatic approach for these complex systems could be to generate a large set of karst conduit network realizations using a pseudo-genetic approach such as SKS, and for each karst realization, flow and transport parameters could be optimized using a gradient-based search such as the one implemented in PEST.