The neutral red retention assay has been proposed to determine the lysosomal membrane stability in immune cells. Nevertheless, this assay implies many examinations under a microscope at short time intervals and therefore the analysis of few samples. The present study proposes two more rapid, efficient, and sensitive sample analyses using flow cytometry method. Lysosomal presence and lysosomal membrane integrity (LMI) were evaluated on the three-spined stickleback, Gasterosteus aculeatus (L.), a well-described model fish species for aquatic ecotoxicology studies. After development of the two biomarkers, they were validated by ex vivo contamination with endosulfan and copper and by in situ sampling. These immunomarkers were clearly modulated by pollutants and their variations seemed to be correlated with leucocyte mortality. Thus, from a practical point of view, lysosomal presence and LMI may provide novel and efficient means of evaluating immune capacities and indicating the toxic effects of environmental pollution.