Abstract Background The present study aims to improve safety and quality assurance of swimming pools located in Sharkia governorate, Egypt. A total of 144 water samples were collected from eight pools. The water quality of the tested pools was assessed according to national swimming pool quality standards in terms of physiochemical and microbial charac- terization. Microbial contamination was assessed by the detection and enumeration of standard indicator organisms. 16S rDNA sequencing and phylogenetic analysis were utilized for further identifcation of most resistant bacterial iso- late. Antimicrobial susceptibility to various natural potentially antimicrobial agents; including aqueous, alcoholic plant extracts and essential oils was conducted. Both MIC and MBC for tested natural antimicrobial agents were determined. Finally, feld application of the most efective antimicrobial agents was carried out to highlight the cons and pros of their usage in feld, in order to possess a broader scope of both theoretical and practical aspects of this study. Results In terms of physical analysis; 82.9% of tested samples were nonconformed to temperature standard, while 100% were conformed to color and odor. Regarding chemical analysis; 54.3% and 53.3% of samples were nonconformed to alkalinity and combined chlorine, respectively. Assessment of microbial contamination indicated the prevalence of Pseudomonas aeruginosa as a main contaminator of tested pool water (57.1%) followed by total coliforms which ranked second among detected microorganisms (52.4%). Upon performing antimicrobial suscepti- bility testing of plant extracts and essential oils, cinnamon hot water extract and essential oil showed narrowest MIC ranges. Upon testing various combinations between diferent tested antimicrobial agents, combination of cinna- mon hot water extract and clove essential oil was identifed as a promising synergetic combination against resistant isolates. In feld application of the most efective antimicrobial compounds resulted in that compatibility markedly decreased for physical standards and slightly for chemical standards. However, microbial pollution was totally elimi- nated after treatment, which was considered and discussed within the context of the study. Conclusion This study targeted full assessment of pools water in Egypt, one of the most prominent fndings of this study is prevalence of P. aeruginosa as the main resistant microorganism responsible for microbial pollution of pool water. Cinnamon hot water extract and clove essential oil were identifed as the most efective natural antimicrobial agents used in the study. Field application of these antimicrobial agents was a signifcant step confrming the valid- ity and credibility of current results highlighting the pros and cons of practical application of the suggested pool decontaminators. Keywords Swimming pools, Physicochemical characteristics, Microbial contamination, Plant extracts, Essential oils