This study focuses on the evaluation of the antimicrobial activity of essential oils (EOs) from medicinal plants against Pseudomonas sp isolated from aquatic environments, and proves its controlling efficacy on Pseudomonas aeruginosa-Dahp1 using Confocal Laser scanning Microscopy. Twenty-seven Pseudomonas spp. (Ps 1–Ps 27) were isolated using King's B medium and the selected P. aeruginosa-Dahp1 was confirmed using 16S r-DNA methods. Antimicrobial activity of 10 EOs was determined using agar well and disc diffusion methods. Ten EOs were extracted with six solvents and the crude extracts were tested against the Pseudomonas spp. through disc diffusion method. Among 10 EOs tested, maximum inhibitory activity was noted in EOs of Wringtia tinctoria against the P. aeruginosa-Dahp1 in the disc diffusion method. The MIC values (concentrations were expressed in Weight/Volume) of the EOs range from 0.5 to 9.054 mg mL−1. The EO of W. tinctoria showed the maximum activity at the concentration (w/v) of 2.060 mg mL−1. The EO of W. tinctoria with chloroform extract showed the maximum inhibition against P. aeruginosa-Dahp1. The CLSM proves the control and viability of 1 × 105 CFU mL−1 of P. aeruginosa-Dahp1 at a lower concentration (2.720 mg) of EOs with chloroform extracts of W. tinctoria. This study pivots for designing of new drugs using EOs of W. tinctoria against Pseudomonades in the aquaculture sites.