The leakage of sewage and agricultural drains has led to the contamination of freshwater branches with toxic heavy elements. This raises concerns about their toxic effects on aquatic ecosystems, especially on fish. Tilapia is regarded as an important protein source in Egypt and many other countries. The biophysical, nutritional, and histological aspects of water pollution in the El-Rahawy and Al-Qatta locations of the Nile on Nilotic tilapia muscle were evaluated by assessing the level of contamination of Nilotic tilapia fish. The current study showed that water of the Rosetta branch water was polluted with a very high level at El-Rahawy Drain discharge (RD) location, and with a high level at Al-Qatta (Q) location, while El-Rahawy (R) location was polluted with a lower level. The study traced the pollution effects on Tilapia (Nilotic) muscles in the previous locations. Bioaccumulation factor (BAF) showed a high value of all heavy metals in Tilapia muscle at the Q and R locations. Contrary to what was expected, discharge (RD) location contamination caused BAF increment of heavy metals in Tilapia muscles at upstream R location. All these results were compared with measured dielectric parameters of Tilapia muscle samples in the frequency range (0.02–1000) kHz. There was an increase in conductivity (σac), dielectric constant (ε′), dielectric loss (ε″), penetration depth (dp), and dissipated power (PD) values of Tilapia muscle, with increasing pollution level. The values of permittivity at low and high frequencies (ε′s & ε′∞) for Tilapia muscle decreased by increasing pollution. Finally, the variation of these parameters, based on that proportionality relationship, can be considered as a physical indicator for fish contamination affected by their environment pollution, although these parameters need further studies in a controlled (qualitatively and quantitatively) polluted media.