The invention discloses a method and a system for sampling aquaculture waters in ponds in real time. The method comprises that: a suite of data acquisition units orderly acquire a plurality of paths of fed samples of the different ponds and different sampling points, namely, orderly sample and monitor the second path and the next plurality of paths of fed samples after finishing sampling and monitoring the first path of fed samples, and start from the first path to perform the next round of sampling and monitoring after the first round of sampling and monitoring is finished; and the data acquisition units transmit monitoring data obtained by the sampling of each round and each path to a central control system in real time, wherein the sampling and monitoring data comprises the concentration of dissolved oxygen DO, a pH value, salinity Sal and temperature Tem. The method and the system have the characteristics of low input cost and good economical efficiency, are specifically suitable for aquaculture in the ponds, and can fully ensure that every time sampling data represents the actual conditions of the aquaculture waters in real time due to the adoption of the monitoring mode of in-vicinity sampling and monitoring and data remote transmission, enable managers to timely master real-time water quality data and take corresponding measures, and reduce the damage of the quality change of the aquaculture waters to aquatic products.