The aquatic application of the eddy correlation (EC) technique is growing more popular and is gradually becoming a standard method for resolving benthic O2 fluxes. By including the effects of the local hydrodynamics, the EC technique provides greater insight into the nature of benthic O2 exchange than traditional methods (i.e., benthic chambers and lander microprofilers). The growing popularity of the EC technique has led to a greater demand for easily accessible and robust EC instrumentation. Currently, the EC instrumentation is limited to two commercially available systems that are still in the development stage. Here, we present a robust, open source EC picoamplifier that is simple in design and can be easily adapted to both new and existing acoustic Doppler velocimeters (ADV). The picoamplifier has a response time of < 0.1 ms and features galvanic isolation that ensures very low noise contamination of the signal. It can be adjusted to accommodate varying ranges of microelectrode sensitivity as well as other types of amperometric microelectrodes. We show that the extracted flux values are not sensitive to reduced microelectrode operational ranges (i.e., lower resolution) and that no signal loss results from using either a 16- or 14-bit analog-to-digital converter. Finally, we demonstrate the capabilities of the picoamplifier with field studies measuring both dissolved O2 and H2S EC fluxes. The picoamplifier presented here consistently acquires high-quality EC data and provides a simple solution for those who wish to obtain EC instrumentation.