This study presents monitoring data about Persistent Organic Pollutants (POPs) into the surface water, air, soil and dust from the Indus Flood-Plain Pakistan and assessment of ecological health impacts on the aquatic life. The sampling campaigns were conducted at 17 sites throughout the stretch of Indus River (approximately 1300 km), starting from high altitudinal northern colder areas followed by lesser Himalayans areas and then through agriculture plains and ending into southern coastal areas. Additionally, health impacts of dichlorodiphenyl trichloroethane (DDE) (major detected contaminant in the Indus River Flood-Plain) were studied using the fish model (Fathead minnow) exposed to DDE, Lipopolysaccharides (LPS), Polyinosinic:polycytidylic acid (Poly IC) and immune end points were measured. The soil and dust samples were collected and passive water sampler and passive air sampler were installed along the Indus River stretch, during 2014. All the samples were extracted (as described in detail in the methodology section) and analyzed by using Gas chromatograph-mass spectrometry (GC-MS). The levels of studied OCPs in the Indus River ranged from 33.75-1553 pg/L (as dissolved phase) and 75.67-560 pg/m3 (as gaseous phase). Among the detected OCPs, dichlorodiphenyl trichloromethane (DDTs) were the dominant chemical and the levels were 0.48-224.2 pg/L as dissolved phase and 32.7-413 pg/m3 as gaseous phase. p,p′-DDE accounted major portion (55-63%) among studied DDTs (both gaseous and dissolved phase), followed by p,p′-DDT (25-20%) throughout the study area. However, the order of occurrence for other studied OCPs was as follows; hexachlorobenzene (HCB), Endosulfans, Chlordanes, and hexachlorocylohexane (HCHs), in descending order, throughout the studied stretch. The dissolved (pg/L) and gaseous (pg/m3) ∑OCPs showed spatial variability (p < 0.05) into various studied zones as; surface water of Alluvial Riverine Zone (ARZ) showed the considerable levels (114) followed by Frozen Mountain Zone (FMZ) (52.9), Low Lying Zone (LLZ) (28.73) and Wet Mountain Zone (WMZ) (14.43), while atmosphere of WMZ showed higher levels (345) followed by ARZ (188), LLZ (70) and FMZ (39), respectively. xii The levels of ∑21 PCBs ranged from 3-226 as dissolved phase (pg/L) and 10-1108 as gaseous phase (pg/m3). However, zone wise PCBs data did not exhibit significant differences (p > 0.05). The trends of OCPs into surface soil follow the order as ∑DDTs > ΣHCHs > heptachlor > other OCPs and in deposited dust as ∑DDTs > ∑HCHs > HCB > Chlordane > other OCPs. In surface soil and deposited dust samples, the average concentrations (ng/g) for ∑DDTs were 26.68 and 7.17 and ΣHCHs were 0.19 and 0.68, respectively. Among DDTs, p, p′-DDT was contributed up to 50% of total DDTs in both soil (14.72 ng/g) and dust (4.28 ng/g), respectively. The levels of ΣPCBs (ng/g, dry weight) were 5.34 and 16.17 in soil and dust, respectively. The spatial patterns of OCPs and PCBs emissions via soil and dust particles into the different studied zones showed that higher ΣOCPs concentrations (ng/g) were measured into dust samples (p < 0.05) collected from WMZ, followed by ARZ, LLZ and FMZ in descending order. Nevertheless, PCBs and HCB were found to be significantly higher (p > 0.05) in the LLZ, which is a consequence of rapid urbanization and/or industrial activities. The indicative diagnostic ratio for DDTs and HCHs suggested recent emission of DDTs as well as historical emission of both chemicals in the regions where they were used for crop protection and malarial control. The PCBs compositional profiles suggested aroclor -1242, -1248, -1254 commercial mixtures as a source of PCBs into surface soil and deposited dust. However, a few exceptions of samples from urban areas that reflected the use of aroclor-1260, and-1262 and/or unintentional leakage from several industrial processes. The principal component analysis/multiple linear regression (PCA/MLR) results showed that pesticides usage in crop/orchard fields and health sector, electric & electronic materials, widespread industrial activities, and Long Range Atmospheric Transport (LRAT) as the main source of OCPs and PCBs in all studied zones. Air-Water and Air-Soil exchange indices also highlighted that LRAT of POPs occurred in colder areas (FMZ) of Pakistan, which act as secondary source of POPs in these areas and may be released by snow meltdown during summer season.The results of present study have provided a baseline data of OCPs and PCBs in Indus Flood-Plain Pakistan and highlighted the moderate to severe OCPs and PCBs contamination into Indus River Flood-Plain, and their huge impact on the living organisms including human and fish. Public awareness is essential, and recommend immediate inspection of the industries and other sources that discharge POPs into the environment as xiii well as an evaluation of the effectiveness of the implementation of the Stockholm Convention’s strict regulations of POPs emissions in Pakistan. According to risk assessment data, dissolved, gaseous, and particulate POPs fractions into the Indus River system have potential to bioaccumulate due to their lipophilic characteristics (log Kow) and even at very low levels, contributed significantly towards the total body burdens into the aquatic organisms (fish) and pose several health risks. The results showed that OCPs and PCBs contaminated dust/soil ingestion, followed by contaminated water intake and air inhalation, played an important role towards the considerable cancer/non-cancer risk (HI and CR values) along the Indus River Flood-Plain. Human risk assessment analysis of contaminated dust showed that DDTs (noticeably p,p′DDE, p,p′-DDT) and PCBs are major constituent chemicals of concern with regard to the development of cancer in children, with ingestion being the main route of exposure of dustborne DDTs (0.12–1.03 × 10−6) and PCBs (0.86–12.43 × 10−6). The WHO05-TEQ values for mono-ortho dioxin-like PCBs (-105, -114, -118, and -156) and non-ortho dioxin like PCBs (−77, −126, −169) were also calculated and ranged from 0.07–0.25 and 0.9–34.5 into the deposited dust and 0.001–0.019 and 1.12–152.7 pg/TEQ/g dw for soil samples, respectively. Among individual mono-ortho DL-PCBs and non-ortho DL-PCBs, PCB-118 and -126 contributed significantly to the total calculated TEQs for the studied soil/dust samples. In order to further assess the risk of DDE (major contaminant along Indus river), the fish model (Fathead minnow) was used and immune effects has been studied. The results showed that there was increased response of neutrophils by the introduction of LPS and Poly-IC to fish model (Fathead minnow) while there was reduction in the number of neutrophils by exposure to DDE and there was also a slight reduction in Fathead minnows exposed to both DDE + LPS and DDE + Poly-IC in both blood and kidney tissue. Hence, DDE may suppress the immune competence of Fathead minnow (fish Model) and lead to increases in the disease susceptibility and mortality of fish, which is a new angle of research.