The invention relates to a shipborne automatic water quality sampler, which mainly includes a sample collector and a sample storage box. The sample collector is composed of a support frame, a suspension device, a sample suction device, a sampling bucket and a controller. The sample storage box consists of a storage box body, a sample bottle and a sample splitter. The sample collector and sample storage box of the shipborne automatic water quality sampler adopts a split structure, can be suitable for installation and use by various manned and unmanned ships. Water quality samples of different depths can be collected into a designated sample bottle automatically, thus improving the automation level and sampling efficiency of water quality sampling work. The sampling bucket has a sampling way identical to manual sampling, a water sample at the position where the bucket is located can be acquired precisely, and the objectivity and accuracy of the sampling result can be effectively guaranteed.