This thesis aims to contribute to the development of sensors and components for Lab-on-a-Chip (LOC) applications at low cost, pursuing sensor autonomy, in order to be able to achieve microfluidic devices for in-situ analysis. These sensors and components will be fabricated by rapid prototyping techniques with integrated smart materials. These smart materials are in some cases used as the sensing area where the analyte can be detected and, in other cases, the materials will act as active components that perform actuation for fluid control and handling in the microfluidic device. In order to prove the suitability of the developed systems, each microfluidic device will be designed and tested with the intention to be used in real environmental scenarios. Therefore, the aim of this thesis is to investigate different aspects of microfluidic technology, such as microfluidic fabrication, microactuators and sensors integration, combining microtechnology and materials science, in order to generate autonomous analytical systems for the continuous monitoring of water quality (e.g. detection of bacteria and nutrients).