Microcystins are toxic microalgae metabolites that exert adverse effects on human and environmental health. Rapid and sensitive analytical techniques for their control are in increasing demand. Here, three immunochromatographic assay formats were developed and compared for the detection of microcystin-LR (MC-LR), the predominant microcystin variant. These assay formats incorporated either direct labeling with antibodies conjugated with gold nanoparticles or indirect labeling via anti-species antibodies or via the biotin–streptavidin interaction. The best sensitivity and stability were obtained with the indirect labeling formats. The limit of instrument detection of the indirect immunochromatographic assay was 0.2 ng mL⁻¹, while the limit of visual detection was 1 ng mL⁻¹. The latter value corresponds to the maximum permissible value of MC-LR in drinking water as determined by the World Health Organization. The developed test system was successfully applied to MC-LR detection in fish samples, which required brief sample preparation, and water samples, which did not require any sample preparation. The assay analysis time was 20 minutes. The rapidity and simplicity of the proposed immunochromatographic method suggest that it is an effective tool for the large-scale screening and control of microcystins.