Nervous necrosis virus (NNV) continues to challenge aquaculture health management, where diagnosis commonly relies on tissue collection, laboratory instrumentation, and trained personnel. Such requirements make routine, non-destructive surveillance difficult in production environments. A microfluidic RT-RPA–LFD platform was therefore combined with machine-learning-assisted sampling-site selection for direct detection of NNV in culture water. Test-line signals were interpreted by RGB analysis, while sampling locations were selected using information on concentration dynamics within the tank. Primer and Mg²⁺ concentrations, reaction temperature, and readout time were optimized before analytical evaluation. The assay remained positive at 2.5 × 10⁻² copies/μL, the lowest nominal NNV concentration tested, whereas neither of the two non-target fish viruses generated a detectable signal. RGB analysis provided a C/T cutoff for binary interpretation. Applied to 30 blind-coded water samples, the cutoff yielded complete agreement with independently assigned reference labels, corresponding to 100% accuracy in this test set. To improve sampling representativeness under dynamic tank conditions, nitrite was used as a hydrodynamic tracer, and five time-series learning models were evaluated for concentration-field prediction. Among the evaluated architectures (LSTM, GRU, ConvLSTM, ConvGRU, and GAN), the GAN produced the smallest prediction error, with concentration deviation remaining below 2 ppm after 12 min. Sampling sites for biological validation were prioritized by combining model forecasts with observed aggregation behavior. In infected-grouper tank trials, NNV was detectable in water from day 4 onward, with infection independently confirmed by RT-qPCR analysis of kidney and spleen tissues. Together, these results establish a non-invasive, data-assisted surveillance framework that may support earlier intervention during emerging viral outbreaks in aquaculture systems.