The vulnerability of karst aquifers to contamination by agrochemical compounds was studied. Such contamination occurs due to its geomorphological structure. Despite the fact, aquifers are important to provide potable water, there is a lack of research about karst aquifers in Brazil. The aim of this study was to evaluate the occurrence of nitrates, fecal coliform bacteria and atrazine in shallow and deep wells in the karst aquifer in the State of Paraná, which is affected by agricultural activities. This study was conducted in an intensive agricultural area located inside the basin of the Upper Iguassu/Ribeira in the Municipality of Colombo, Paraná in Brazil. The sampling campaigns were carried out between 2014 and 2015 in fifteen shallow wells and seven deep wells. Nitrates, total and fecal coliforms and atrazine were analyzed. Nitrates were found in higher concentration in all shallow wells, ranging from 0.14 mg L-1 and 40.22 mg L-1. In deep wells, the lower concentrations were between 1.24 mg L-1 e 17.86 mg L-1. The analysis of total and fecal coliforms showed the bias for nitrates. Atrazine was detected in five shallow wells and in four deep wells. Physico-chemical characteristics of atrazine as well as fractures of the karstic aquifer and high hydraulic conductivity can be considered as determining factors in the fate of pesticides.