Measuring the concentration of different compounds in aquatic ecosystem and understanding their impact on the environment are some of the main objectives in the environmental monitoring field. Trace metals, nutrients, volatile organic compounds (VOCs), biotoxins and algaes are among the most important targets of such assessment. Their quantification at an appropriate time scale is crucial in order to understand their dynamics in the marine biogeochemical processes. In situ continuous monitoring is the key to achieve these objectives. This thesis is focused on the development of new micro-engineered tools for improving the performance of electroanalytical techniques by exploiting microfabrication techniques. The developed devices were fabricated by using different techniques, such as thin-film technology, printing and additive manufacturing techniques. The quantification of nutrients is hampered by the high sodium chloride content present in the seawater. Literature is weak concerning systems which provide a selective removal of chloride with respect to other ions. One of the developed tools of this thesis is an environmentally-friendly microfluidic platform for selective sodium chloride removal prior to nutrients detection: chloride removal occurs upon bulk electrolysis in a thin-layer configuration and a ten times-fold reduction was achieved. Trace metals speciation may vary continuously reflecting changing in aquatic system physicochemical conditions. Their quantification is commonly achieved by voltammetric techniques. Voltammetric probes have been reported in literature for detection of trace metals such as lead, cadmium, copper and zinc. The core of these systems is a miniaturized sensor composed by an array of microelectrodes serving as WE and a CE. The reference electrode is a crucial component for the functioning of such sensors however its integration is still challenging. The second tool developed in the framework of this thesis is a three-electrode on-chip sensor for the detection of trace metals, where RE integration is achieved by using a PVC membrane plasticized with ionic liquids as diffusion barrier on top of a silver/silver chloride electrode. These sensors were capable to detect trace metals, but further improvement is required for their quantification. Marine biotoxins are compounds with toxic activity that accumulate in fish and shellfish. Among the various species of biotoxins, another target of this work is saxitoxin, a low molecular weight neurotoxin. Its detection is hindered by its low concentration, therefore a pre-concentration unit is required. Another herein developed tool is a simple microfluidic platform predisposed for pre-concentration of saxitoxin; its working principle is based on the binding of the saxitoxin to a specific aptamer and its release upon a temperature increase. VOCs, such as hydrocarbons and chlorinated hydrocarbons, are considered as significant indicators of urban and industrial pollution. Mid-infrared fiber-optic evanescent wave sensors constitute one of the most promising approaches for continuous VOCs pollution monitoring in seawater. In this thesis a microfluidic platform designed to optimize the enrichment of the polymer layer coating the fiber with the target analytes is developed. The optimization of the device design allowed the simultaneous detection of ten VOCs species. All the tools developed are intended to be integrated in submersible probes for in situ deployment.