The Qatari mangroves of Al-Khor are being increasingly exposed to a wide variety of anthropogenic pollutants due to land reclamation and urban expansion. In this study, we evaluated the lethal and genotoxic effects of methylmercury, trace metals, and organotins, assessing mortality and aneuploidy levels (abnormal number of chromosomes) in the endemic shrimp Palaemon khori under laboratory conditions. In the experimental design, two different concentrations were used for each family of contaminant (single or combined): an environmental concentration equivalent to the maximum value reported in the environment and a value ten times higher, for a period of eight weeks. Survival decreased significantly when pollutants were administrated in combination, even at environmental concentrations (as shown by Cox proportional hazards ratios): similar levels of mortality would be reached by individual type of pollutants only at ten times the environmental concentration. This critical result, under controlled lab conditions, highlights the importance of monitoring mixtures of contaminant types over single ones in the marine environment. Aneuploidy was reported in all treatments and control ranging from 5% to 19% at week four and from 7% to 21% at week eight. All treatments presented significantly higher aneuploidy levels when compared to the control. However, no significant difference was observed between the two time periods, even though 30% of the treatments could not be assessed at week eight, as not enough animals were still alive. In conclusion, the use of endemic species should be considered a valuable tool to determine local perturbations, representing a regional bioindicator of multiple environmental stressors from the initial stages of contamination.