Compact treatment plants, based on the use of bioreactors enhancing retention of biomass through the growth of biofilms and the use membrane separation (micro and ultrafiltration) have shown to be efficient for conventional and emerging contaminants. We have demonstrated how wastewaters highly loaded in antibiotics and pathogens such as source separated urban wastewater (grey and black fractions; in Demosite 1), industrial wastewaters from antibiotics production (Demosite 2) and hospital effluents (Demosites 3 and 4) could be efficiently treated in anaerobic and hybrid anoxic/aerobic conditions, reaching high removals for COD (>90%) and TN (~70%). In Demosites 1, 3 and 4, the removal of a representative group of antibiotics, including the widely prescribed sulfamethoxazole (SMX), trimethoprim (TMP) and ciprofloxacin (CIP), was in the moderate to high range, which could be further improved by the use of Powdered activated carbon (PAC) in bioreactors. In Demosite 2, wastewater from vancomycin production industry with approximately 0.1-0.2 g/L vancomycin concentration was treated, which implies OMP concentrations of 4 orders of magnitude higher than in the other wastewater. In the case of antibiotic resistant genes (ARGs), removals expressed as difference in relative abundances between the influents and effluents were >70% in all treatment systems. ARGs abundance was especially relevant in sludges and biofilms, highlighting the important barrier that supposes the final membrane. It was shown that ARGs selection correlated with changes in taxonomic assemblies (diversity), either driven by the overall community or by some few genera depending on the overall microbial diversity. In Demosite 2, vancomycin resistant genes were targeted, showing a retention in the sludge and biofilm in the carriers in the first month of pilot plant operation and afterwards a decrease in the proposed treatment strategy. In the final polishing disinfection step, the use of microparticles functionalized with a quaternary ammonium compound showed further beneficial effects against the acquisition of antimicrobial resistance genes. Some operational conditions in the pilot plants operated at the different demosites, such as hydraulic and solid retention time have shown to be parameters that could be adjusted to optimize CEC removals. A water disinfection technology based on the use of functionalised microparticles that avoid the release of biocides in the water stream was studied. Some further removal of antibiotics occurred during such postreatment, although the most outstanding results was the strong reduction in DNA that was achieved (also some further reduction in ARGs was measured). Overall, decentralized treatment at both Demosite I (USC, urban wastewater separated in black and grey fractions) and Demosite 3 (DTU, hospital effluents) efficiently eliminated bacteria and enteric viruses. However, some species (ex. certain Enterococcus spp.) were detected in the final effluents. Analysis of the genomes revealed multiple genes associated with antibiotic resistance, including SMX, TMP and CIP. In the PRESAGE project we also developed new methodologies. A standarised protocol for ARG quantification as well as a gene selection protocol based on empirical and experimental evidence was proposed to allow the detection of highly relevant genes along the different treatment schemes. As from the ecotoxicological point of view, in general the results highlight the effectiveness of various treatment processes, in mitigating toxicity and genotoxicity. The addition of PAC in Demosite 1 proved to be effective in reducing completely genotoxicity. The results support the use of PAC and IFAS-MBR as reliable treatments to reduce environmental risks (Demosites 1-3), as well as the anaerobic system used in Demosite 4 (USP, Brazil). The use of gut microbiota of Xenopus laevis was proposed as methodology that could be used as a standardized test to assess variation of resistome when exposed to substances and or effluent wastewater.