The main objective of this study is to develop molecularly imprinted polymer (MIP) based micro mechanical cantilever sensor system that has high specificity, fast response time and is easily applicable by user for the detection of ciprofloxacin (CPX) molecule in water resources. Highly specific CPX imprinted nanoparticles were synthesized by miniemulsion polymerization technique. The average size of the synthesized nanoparticles was measured about 160 nm with high monodispersivity. Covalent and monolayer binding of the MIP nanoparticles on cantilevers was provided by EDC/NHS activation. Validation of the developed cantilever nanosensor was performed in air with dip-and-dry technique by employing the dynamic sensing mode. According to the results obtained, micromechanical cantilever sensor system worked linearly for the concentration range of 1.5-150.9 mu M. This concentration range resulted with 18.4-48.9 pg mass load on the MIP modified cantilever. The sensitivity of the developed sensor was calculated as 2.6 Hz/pg. To control the specificity of MIPs, a different antibiotic enrofloxacin (ENF), with a similar physical and chemical structure with CPX, was used, which showed 7 folds low binding affinity. The developed highly specific microcantilever sensor has a response time of approximately 2 min and is reusable up to 4 times. The results indicate that the MIP based AFM nanosensor has high sensitivity for the CPX molecule. This combination of MIP nanoparticles with micromechanical sensors is one of the pioneer studies in the mass sensing applications. This fast, low cost and highly sensitive CPX specific MIP nanoparticle based nanosensor developed in this research have the potential to pave the way for further studies. (C) 2016 Elsevier B.V. All rights reserved.