Fiber optic particle plasmon resonance (FOPPR) biosensors have been useful tools to determine a variety of biological samples including viruses with superior detection limits than using conventional ELISA methods. In addition, without using tedious procedures required in ELISA protocols, FOPPR method can minimize contamination interferences and obtain accurate results in timely fashion. FOPPR biosensor is potentially a suitable virus detection device to implement in fish farms. In Taiwan, aquaculture products such as groupers suffer tremendous loss because of ineffective disease prevention efforts. The infected signs are not detected in the early stage before severe outbreak to cause uncontrollable consequences. Therefore when the virus level is low, using highly sensitive FOPPR biosensors to monitor pond water is a promising means to improve the effectiveness of aquatic product disease prevention by taking water treatment actions. We have also developed FOPPR assays to determine nervous necrosis virus (NNV), which cause massively high mortality rate (∼90%) in larva and juvenile stages of grouper species. Using coat proteins of NNV as standards in 2% salt water, the detection limit of 100 ng/mL is obtained. This limit is nearly 2 orders of magnitude lower than that using ELISA assays and adequate to indicate the severance level of NNV outbreak. Ground meat of infected juvenile grouper was diluted with saline to prepare simulated water samples. Ultra-low virus level of 40k TCID50 per mL is found in filtrate. The comparison determination data between using FOPPR and quantitative PCR methods are acceptable too. Unlike RT-PCR method not able to detect NNV RNA in pond water until severe infection, we demonstrate that FOPPR assay can detect NNV in pond water at very low NNV level at early infection stage, a couple of days prior to the outbreak occurrence. We also show that commercial FOPPR biosensor maintains stable immuno-sensing signal readout in indoor aquaculture settings. We will also discuss the potential applications of using FOPPR to monitor grouper larvae pond water to activate biochar filtration equipment when infection sign occurs.