In this work, an optofluidic SERS device optimized for on-site analytics in the field is utilized for the multiplexed detection of three fungicides that are highly regulated in aquaculture. The optofluidic SERS microsystem does not require a bulky pump for sample loading, which significantly improves its portability; the sample is simply loaded into the device by applying negative pressure using a pipette. Moreover, integrated fiber optic cables automate sample excitation and signal collection without the need for alignment on a traditional Raman microscope. The detection zone of the device consists of a porous matrix of packed silica microspheres that accumulates silver nanoparticles and adsorbed analyte molecules. This passive concentration matrix has been shown to boost the SERS signal by up to four orders of magnitude as compared to SERS in an open microfluidic channel. We were able to detect as low as 5 ppm methyl parathion, 0.1 ppb malachite green, and 5 ppb thiram simultaneously.