Demand for new automated analytical procedures and instrumentation for the continuous monitoring of (bio)chemical parameters, such as those affecting water quality, gathers special importance due to the significant consequences that the use or the consumption of (bio)chemically contaminated water might have. µ- Total Analysis Systems or Lab-On-a-Chip devices are increasingly employed with this purpose owing to the high integration and automation of these devices that allow, through miniaturization, the possibility of performing in situ measurements. Besides, the use of nanoparticles with analytical purposes has demonstrated to improve the sensitivity and detection limits of optical methods. Within this general context, the present work is focused on the development of automated analytical microsystems to perform colorimetric or fluorimetric analyses, based on the use of nanoparticles as optical labels, for the rapid detection of water pollutants or organisms, such as heavy metals or bacteria. However, the use of nanoparticles with identical physical characteristics is a must in order to obtain reliable and reproducible analytical measures. Therefore, the first part of this work is addressed to the development of microreactors for the synthesis of metallic, semiconductor and carbon nanoparticles. Seven different ceramic microreactors are developed, in which the influence of the design (dimensions and configuration of the channels) and the hydrodynamic (flow rates and dosage volumes) parameters have been studied. Moreover, a miniaturized optical detection system has been implemented for the in-line monitoring of the synthesis; and a thermal module has been also developed to reach and accurately control temperatures up to 300 ºC for when required. It is important to highlight that all prototypes operate automatically, which simplifies the syntheses and improves the reproducibility of the obtained nanoparticles. The second part focuses on the development of analytical microsystems based on the use of the nanoparticles previously synthesized for water quality analysis. Two different prototypes have been constructed and tested. The first described allows the monitoring of mercuric ion in water. The system is based on the selective recognition of the analyte by an ionophore (a thiourea derivative), attached onto gold nanoparticles surface. The metal-ionophore interaction generates a change on the surface plasmon resonance band of the nanoparticles, resulting in a quantifiable optical signal, which is in-line registered by a miniaturized optical detection system integrated in the microfluidic platform. Once optimized, the device is capable to automatically detect up to 11 ppb of mercuric ion. Finally, and as a first approximation to the use of fluorescent nanoparticles within microsystems, a prototype for the determination of Escherichia coli in water has been developed, which uses the β-galactosidase enzyme as label. This change responds to the necessity of improving the miniaturized optical system (while maintaining its portability and low cost) due to the low sensitivity observed when fluorescent nanoparticles were used as labels, which at the moment is not feasible. An oligonucleotide sandwich assay is performed in the microfluidic system based on the use of a specific oligonucleotide of the pathogen as target. On the other hand, magnetic beads are employed as substrate support of the assay, which allow simplifying and improving the different steps of the procedure, while the enzyme used as probe label generates a coloured product (o-nitrophenol) with the addition of the substrate, which is registered through the miniaturized optical system implemented. Once optimized, the device can detect up to 1 ppb of the target oligonucleotide in only 20 minutes. The presented results demonstrate the great potential of automated analytical microsystems based on the use of nanoparticles for the monitoring of water quality. Similarly, the suitability of microreactors for the synthesis of nanoparticles has been well proved.